From d291093a28ed104756eab4215a407970f793a3c5 Mon Sep 17 00:00:00 2001 From: Katie Stahl Date: Mon, 18 Nov 2024 13:10:58 -0500 Subject: [PATCH] =?UTF-8?q?feat:=20add=20has=5Fai=5Fapplication=20tag=20to?= =?UTF-8?q?=20standard=20collections=20that=20have=20ai=E2=80=A6=20(#126)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * feat: add has_ai_application tag to standard collections that have ai applications * feat: add has_ai_application tag to standard collections that have ai applications * Update schema --------- Co-authored-by: caufieldjh --- project/data/DataStandardOrTool.json | 204 ++++++++++++++---- project/data/DataStandardOrTool.tsv | 136 ++++++------ .../datamodel/standards_schema_all.py | 48 ++++- src/data/DataStandardOrTool.yaml | 93 ++++++++ .../standards_datastandardortool_schema.yaml | 32 ++- 5 files changed, 393 insertions(+), 120 deletions(-) diff --git a/project/data/DataStandardOrTool.json b/project/data/DataStandardOrTool.json index 9aa55f1..6eaf94e 100644 --- a/project/data/DataStandardOrTool.json +++ b/project/data/DataStandardOrTool.json @@ -49,7 +49,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:1" @@ -148,6 +149,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:9", "B2AI_TOPIC:15" @@ -169,7 +173,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "guidelines" + "guidelines", + "has_ai_application" ], "has_relevant_organization": [ "B2AI_ORG:4" @@ -268,7 +273,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:4" @@ -510,7 +516,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:20" @@ -633,7 +640,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:20" @@ -657,7 +665,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:22" @@ -935,7 +944,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:4" @@ -957,7 +967,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:4" @@ -1108,7 +1119,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:4", @@ -1227,7 +1239,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -1247,7 +1260,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -1560,7 +1574,8 @@ "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ "audiovisual", - "fileformat" + "fileformat", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:15" @@ -1602,6 +1617,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1622,6 +1640,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1642,6 +1663,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1662,6 +1686,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1682,6 +1709,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1702,6 +1732,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1722,6 +1755,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1742,6 +1778,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1762,6 +1801,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1783,6 +1825,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1803,6 +1848,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1823,6 +1871,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1843,6 +1894,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1863,6 +1917,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1883,6 +1940,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1903,6 +1963,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1923,6 +1986,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -1943,6 +2009,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -2508,7 +2577,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:13" @@ -3814,7 +3884,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:11" @@ -4440,7 +4511,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:1" @@ -4514,7 +4586,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:22" @@ -4733,7 +4806,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:4" @@ -4757,7 +4831,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:4" @@ -4905,7 +4980,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:9" @@ -5005,7 +5081,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:4" @@ -5321,7 +5398,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:9" @@ -5361,7 +5439,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:12", @@ -5444,7 +5523,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:12", @@ -5718,7 +5798,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "has_relevant_organization": [ "B2AI_ORG:93" @@ -6920,7 +7001,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "fileformat" + "fileformat", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -6982,7 +7064,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "fileformat" + "fileformat", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -7944,6 +8027,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:5" ], @@ -9223,6 +9309,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:5" ], @@ -13311,6 +13400,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:19" ], @@ -13389,6 +13481,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "concerns_data_topic": [ "B2AI_TOPIC:15" ], @@ -13601,6 +13696,9 @@ "contributor_name": "Harry Caufield", "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", + "collection": [ + "has_ai_application" + ], "has_relevant_organization": [ "B2AI_ORG:25" ], @@ -13716,7 +13814,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "standardsregistry" + "standardsregistry", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -13988,7 +14087,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "machinelearningframework" + "machinelearningframework", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -14428,7 +14528,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -14627,7 +14728,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "machinelearningframework" + "machinelearningframework", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -14794,7 +14896,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "machinelearningframework" + "machinelearningframework", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -14857,7 +14960,8 @@ "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ "graphdataplatform", - "machinelearningframework" + "machinelearningframework", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:21" @@ -14933,7 +15037,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "multimodal" + "multimodal", + "has_ai_application" ], "purpose_detail": "A unified Holistic AI in Medicine (HAIM) framework to facilitate the generation and testing of AI systems that leverage multimodal inputs.", "is_open": true, @@ -15226,7 +15331,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "machinelearningframework" + "machinelearningframework", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -15344,7 +15450,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "machinelearningframework" + "machinelearningframework", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -15578,7 +15685,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "scrnaseqanalysis" + "scrnaseqanalysis", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:34" @@ -15768,7 +15876,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "machinelearningframework" + "machinelearningframework", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -15849,7 +15958,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "machinelearningframework" + "machinelearningframework", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -16055,7 +16165,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "machinelearningframework" + "machinelearningframework", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -16118,7 +16229,8 @@ "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ "deprecated", - "machinelearningframework" + "machinelearningframework", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -16282,7 +16394,8 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "ORCID:0000-0001-5705-7831", "collection": [ - "machinelearningframework" + "machinelearningframework", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -16732,7 +16845,8 @@ "contributor_orcid": "ORCID:0000-0001-5705-7831", "contribution_date": "2023-05-23", "collection": [ - "datamodel" + "datamodel", + "has_ai_application" ], "concerns_data_topic": [ "B2AI_TOPIC:5" @@ -16902,7 +17016,8 @@ "contributor_orcid": "0000-0001-5705-7831", "contribution_date": "2023-09-25", "collection": [ - "minimuminformationschema" + "minimuminformationschema", + "has_ai_application" ], "purpose_detail": "A schema designed to allow rapid replication of the technical design process of a clinical AI study.", "is_open": true, @@ -16949,6 +17064,9 @@ "contributor_github_name": "caufieldjh", "contributor_orcid": "0000-0001-5705-7831", "contribution_date": "2024-11-02", + "collection": [ + "has_ai_application" + ], "purpose_detail": "A universal catalog for data and AI", "is_open": true, "requires_registration": false, diff --git a/project/data/DataStandardOrTool.tsv b/project/data/DataStandardOrTool.tsv index e4922ea..1f16570 100644 --- a/project/data/DataStandardOrTool.tsv +++ b/project/data/DataStandardOrTool.tsv @@ -1,18 +1,18 @@ id category name description contributor_name contributor_github_name contributor_orcid collection concerns_data_topic purpose_detail is_open requires_registration url formal_specification has_relevant_organization publication subclass_of contribution_date [B2AI_STANDARD:1](DataStandardOrTool.markdown) BiomedicalStandard .ACE format .ACE format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) The ACE file format is a specification for storing data about genomic contigs. The original ACE format was developed for use with Consed, a program for viewing, editing, and finishing DNA sequence assemblies. ACE files are generated by various assembly programs, including Phrap, CAP3, Newbler, Arachne, AMOS (sequence assembly) (more specifically Minimo) and Tigr Assembler v2. True False https://en.wikipedia.org/wiki/ACE_(genomic_file_format) https://web.archive.org/web/20100609072313/http://bcr.musc.edu/manuals/CONSED.txt [B2AI_STANDARD:2](DataStandardOrTool.markdown) BiomedicalStandard DMS 2023 NIH Data Management and Sharing Policy Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [policy] NIH has issued the Data Management and Sharing (DMS) policy (effective January 25, 2023) to promote the sharing of scientific data. Sharing scientific data accelerates biomedical research discovery, in part, by enabling validation of research results, providing accessibility to high-value datasets, and promoting data reuse for future research studies. Under the DMS policy, NIH expects that investigators and institutions do the following. Plan and budget for the managing and sharing of data, Submit a DMS plan for review when applying for funding, Comply with the approved DMS plan. True False https://sharing.nih.gov/data-management-and-sharing-policy/about-data-management-and-sharing-policy/data-management-and-sharing-policy-overview [[B2AI_ORG:67]](Organization.markdown) -[B2AI_STANDARD:3](DataStandardOrTool.markdown) BiomedicalStandard ABCD Access to Biological Collections Data Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:1]](DataTopic.markdown) The Access to Biological Collections Data (ABCD) Schema is an evolving comprehensive standard for the access to and exchange of data about specimens and observations (a.k.a. primary biodiversity data). The ABCD Schema attempts to be comprehensive and highly structured, supporting data from a wide variety of databases. It is compatible with several existing data standards. Parallel structures exist so that either (or both) atomised data and free-text can be accommodated. Version 1.2 is currently in use with the GBIF (Global Biodiversity Information Facility) and BioCASE (Biological Collection Access Service for Europe) networks. Apart from the GBIF and BioCASE networks, the potential for the application of ABCD extends to internal networks, or in-house legacy data access (e.g. datasets from external sources that shall not be converted and integrated into an institution's own data, but be kept separately, though easily accessible). By defining relations between terms, ABCD is a step towards an ontology for biological collections. True False https://abcd.tdwg.org/ [[B2AI_ORG:93]](Organization.markdown) +[B2AI_STANDARD:3](DataStandardOrTool.markdown) BiomedicalStandard ABCD Access to Biological Collections Data Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:1]](DataTopic.markdown) The Access to Biological Collections Data (ABCD) Schema is an evolving comprehensive standard for the access to and exchange of data about specimens and observations (a.k.a. primary biodiversity data). The ABCD Schema attempts to be comprehensive and highly structured, supporting data from a wide variety of databases. It is compatible with several existing data standards. Parallel structures exist so that either (or both) atomised data and free-text can be accommodated. Version 1.2 is currently in use with the GBIF (Global Biodiversity Information Facility) and BioCASE (Biological Collection Access Service for Europe) networks. Apart from the GBIF and BioCASE networks, the potential for the application of ABCD extends to internal networks, or in-house legacy data access (e.g. datasets from external sources that shall not be converted and integrated into an institution's own data, but be kept separately, though easily accessible). By defining relations between terms, ABCD is a step towards an ontology for biological collections. True False https://abcd.tdwg.org/ [[B2AI_ORG:93]](Organization.markdown) [B2AI_STANDARD:4](DataStandardOrTool.markdown) BiomedicalStandard AGP AGP format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) AGP format describes the assembly of a larger sequence object from smaller objects. The large object can be a contig, a scaffold (supercontig), or a chromosome. Each line (row) of the AGP file describes a different piece of the object, and has the column entries defined below. Extended comments follow. It does not serve for either a description of how sequence reads were assembled, or a description of the alignments between components used to construct a larger object. Not all of the information in proprietary assembly files can be represented in the AGP format. It is also not for recording the spans of features like repeats or genes. True False https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/ [B2AI_STANDARD:5](DataStandardOrTool.markdown) BiomedicalStandard AnIML Analytical Information Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:3]](DataTopic.markdown) The Analytical Information Markup Language (AnIML) is the emerging ASTM XML standard for analytical chemistry data. It is currently in pre-release form. It is a combination of a highly flexible core schema that defines XML tagging for any kind of analytical information; A set of technique definition documents. These XML files, one per analytical technique, apply tight constraints to the flexible core and in turn are defined by the Technique Schema; Extensions to Technique Definitions are possible to accommodate vendor- and institution-specific data fields. Mission Statement Our goal is to serve as the open-source development platform for a new XML standard for Analytical Chemistry Information. The project is a collaborative effort between many groups and individuals and is sanctioned by the ASTM subcommittee E13.15. http://animl.cvs.sourceforge.net/viewvc/animl/schema/animl-core.xsd True False https://www.animl.org/ [[B2AI_ORG:8]](Organization.markdown) [B2AI_STANDARD:6](DataStandardOrTool.markdown) BiomedicalStandard ARRIVE Animal Research Reporting In Vivo Experiments Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] Guidelines intended to improve the reporting of animal experiments. True False https://arriveguidelines.org/ doi:10.1371/journal.pbio.3000411 [B2AI_STANDARD:7](DataStandardOrTool.markdown) BiomedicalStandard aECG Annotated ECG standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:37]](DataTopic.markdown) Provides a common means of electronically storing both the ECG wave form and associated annotations. True False https://www.hl7.org/implement/standards/product_brief.cfm?product_id=70 [[B2AI_ORG:40]](Organization.markdown) -[B2AI_STANDARD:8](DataStandardOrTool.markdown) BiomedicalStandard AIM Annotation and Image Markup schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:9|B2AI_TOPIC:15]](DataTopic.markdown) The Annotation and Image Markup project provides a standardized schema for capturing the results of medical imaging exams, primarily radiology, using controlled terminologies/ontologies. AIM captures results in terms of the region within an image in which areas of interest are located, the semantic descriptions of those regions, inferences about them, calculations on them, and quantitative features derived by computer programs run on them. AIM is interoperable with DICOM-SR and HL7-CDA, other standards for image metadata, but it provides unique advantages by providing an explicit semantic model of imaging results. True False https://github.com/NCIP/annotation-and-image-markup [[B2AI_ORG:71]](Organization.markdown) -[B2AI_STANDARD:9](DataStandardOrTool.markdown) BiomedicalStandard ANSI/CTA-2090 ANSI/CTA Standard - The Use of Artificial Intelligence in Health Care Trustworthiness Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] AI in healthcare; three major expressions of how trust is created and maintained - Human Trust, Technical Trust, and Regulatory Trust. False False https://shop.cta.tech/collections/standards/products/the-use-of-artificial-intelligence-in-healthcare-trustworthiness-cta-2090 [[B2AI_ORG:4]](Organization.markdown) +[B2AI_STANDARD:8](DataStandardOrTool.markdown) BiomedicalStandard AIM Annotation and Image Markup schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:9|B2AI_TOPIC:15]](DataTopic.markdown) The Annotation and Image Markup project provides a standardized schema for capturing the results of medical imaging exams, primarily radiology, using controlled terminologies/ontologies. AIM captures results in terms of the region within an image in which areas of interest are located, the semantic descriptions of those regions, inferences about them, calculations on them, and quantitative features derived by computer programs run on them. AIM is interoperable with DICOM-SR and HL7-CDA, other standards for image metadata, but it provides unique advantages by providing an explicit semantic model of imaging results. True False https://github.com/NCIP/annotation-and-image-markup [[B2AI_ORG:71]](Organization.markdown) +[B2AI_STANDARD:9](DataStandardOrTool.markdown) BiomedicalStandard ANSI/CTA-2090 ANSI/CTA Standard - The Use of Artificial Intelligence in Health Care Trustworthiness Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines|has_ai_application] AI in healthcare; three major expressions of how trust is created and maintained - Human Trust, Technical Trust, and Regulatory Trust. False False https://shop.cta.tech/collections/standards/products/the-use-of-artificial-intelligence-in-healthcare-trustworthiness-cta-2090 [[B2AI_ORG:4]](Organization.markdown) [B2AI_STANDARD:10](DataStandardOrTool.markdown) BiomedicalStandard AB1 Applied Biosystems sequence read binary format file Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) A binary version of raw DNA sequence reads from Applied Biosystems sequencing analysis software. Also known as ABIF. False False https://projects.nfstc.org/workshops/resources/articles/ABIF_File_Format.pdf [B2AI_STANDARD:11](DataStandardOrTool.markdown) BiomedicalStandard ABI Applied Biosystems sequence read binary format file Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) A binary version of raw DNA sequence reads from Applied Biosystems sequencing analysis software. False False https://tools.thermofisher.com/content/sfs/manuals/4346366_DNA_Sequenc_Analysis_5_1_UG.pdf [B2AI_STANDARD:12](DataStandardOrTool.markdown) BiomedicalStandard ARB ARB software binary alignment format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) A binary alignment format used by the ARB package. True False http://www.arb-home.de/documentation.html doi:10.1093/nar/gkh293 [B2AI_STANDARD:13](DataStandardOrTool.markdown) BiomedicalStandard ADL Archetype Definition Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:9]](DataTopic.markdown) ADL is designed as an abstract human-readable and computer-processible syntax. ADL archetypes can be hand-edited using a normal text editor. The intended audience includes standards bodies producing health informatics standards; Academic groups using openEHR; The open source healthcare community; Solution vendors; Medical informaticians and clinicians interested in health information. True False https://specifications.openehr.org/releases/AM/latest/ADL1.4.html [[B2AI_ORG:79]](Organization.markdown) -[B2AI_STANDARD:14](DataStandardOrTool.markdown) BiomedicalStandard StructureDefinition-argo-careplan Argonaut Data Query Implementation Guide Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:4]](DataTopic.markdown) Specifications for sharing single sets of patient care plans. Based on FHIR R2. True False http://www.fhir.org/guides/argonaut/r2/StructureDefinition-argo-careplan.html [[B2AI_ORG:40]](Organization.markdown) +[B2AI_STANDARD:14](DataStandardOrTool.markdown) BiomedicalStandard StructureDefinition-argo-careplan Argonaut Data Query Implementation Guide Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:4]](DataTopic.markdown) Specifications for sharing single sets of patient care plans. Based on FHIR R2. True False http://www.fhir.org/guides/argonaut/r2/StructureDefinition-argo-careplan.html [[B2AI_ORG:40]](Organization.markdown) [B2AI_STANDARD:15](DataStandardOrTool.markdown) BiomedicalStandard AMIS Article Minimum Information Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [minimuminformationschema] [[B2AI_TOPIC:16]](DataTopic.markdown) The curation process is significantly slowed down by missing information in the articles analyzed. The identity of the clones used to generate ISH probes and the precise sequences tested in reporter assays constituted the most frequent omissions. To help authors ensure in the future that necessary information is present in their article, the Article Minimum Information Standard (AMIS) guidelines have been defined. The guideline describes the mandatory (and useful) information that should be mentioned in literature articles to facilitate the curation process. These guidelines extend the minimal information defined by the MISFISHIE format (Deutsch at al. 2008, Nature Biotechnology). True False doi:10.1038/npre.2010.5054.1 [B2AI_STANDARD:16](DataStandardOrTool.markdown) BiomedicalStandard Axt Axt Alignment Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) A format for sequence alignments. True False https://genome.ucsc.edu/goldenPath/help/axt.html [B2AI_STANDARD:17](DataStandardOrTool.markdown) BiomedicalStandard BAI BAM indexing format file Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) A file containing the index for a Binary Alignment Map (BAM) file. True False https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial6/ @@ -24,14 +24,14 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:23](DataStandardOrTool.markdown) BiomedicalStandard 2bit Binary sequence information Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) A .2bit file stores multiple DNA sequences (up to 4 Gb total) in a compact randomly-accessible format. The file contains masking information as well as the DNA itself. True False http://genome.ucsc.edu/FAQ/FAQformat.html#format7 [B2AI_STANDARD:24](DataStandardOrTool.markdown) BiomedicalStandard BCF Binary variant call format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) A binary version of the variant call format (VCF). True False https://samtools.github.io/bcftools/bcftools.html [B2AI_STANDARD:25](DataStandardOrTool.markdown) BiomedicalStandard BioCompute BioCompute Object standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:1]](DataTopic.markdown) Because of the many different ways to organize data, a major goal of the BioCompute project is to build and maintain a formal standard through recognized, accredited standards setting organizations like the Institute for Electrical and Electronics Engineers (IEEE) and the International Standards Organization (ISO). A formal, consensus-based standard builds predictability and even more stability into the way in which bioinformatic methods are communicated. The standard, officially known as 2791-2020, has two parts, the standards document and the schema, which is maintained in an open source repository. True False https://docs.biocomputeobject.org/user_guide/ [[B2AI_ORG:44]](Organization.markdown) doi:10.5731/pdajpst.2016.006734 -[B2AI_STANDARD:26](DataStandardOrTool.markdown) BiomedicalStandard Biolink Biolink Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:20]](DataTopic.markdown) A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. True False https://biolink.github.io/biolink-model/ [[B2AI_ORG:70]](Organization.markdown) doi:10.1111/cts.13302 +[B2AI_STANDARD:26](DataStandardOrTool.markdown) BiomedicalStandard Biolink Biolink Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:20]](DataTopic.markdown) A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. True False https://biolink.github.io/biolink-model/ [[B2AI_ORG:70]](Organization.markdown) doi:10.1111/cts.13302 [B2AI_STANDARD:27](DataStandardOrTool.markdown) BiomedicalStandard BEL Biological Expression Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] A language for representing scientific findings in the life sciences in a computable form. True False https://bel.bio/ https://language.bel.bio/ [B2AI_STANDARD:28](DataStandardOrTool.markdown) BiomedicalStandard BRIDG Model Biomedical Research Integrated Domain Group Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 The Biomedical Research Integrated Domain Group (BRIDG) Model is a collaborative effort engaging stakeholders from the Clinical Data Interchange Standards Consortium (CDISC), the HL7 BRIDG Work Group, the US National Cancer Institute (NCI), and the US Food and Drug Administration (FDA). The goal of the BRIDG Model is to produce a shared view of the dynamic and static semantics for the domain of basic, pre-clinical, clinical, and translational research and its associated regulatory artifacts. True False https://bridgmodel.nci.nih.gov/ https://github.com/CBIIT/bridg-model/ [[B2AI_ORG:15|B2AI_ORG:31|B2AI_ORG:40|B2AI_ORG:71]](Organization.markdown) doi:10.1093/jamia/ocx004 [B2AI_STANDARD:29](DataStandardOrTool.markdown) BiomedicalStandard BioPAX BioPAX standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:21]](DataTopic.markdown) BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap. True False http://www.biopax.org/ doi:10.1038/nbt.1666 [B2AI_STANDARD:30](DataStandardOrTool.markdown) BiomedicalStandard Bioschemas Bioschemas Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:1]](DataTopic.markdown) Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. True False https://bioschemas.org/ https://github.com/BioSchemas/specifications [[B2AI_ORG:28]](Organization.markdown) [B2AI_STANDARD:31](DataStandardOrTool.markdown) BiomedicalStandard BRISQ Biospecimen Reporting for Improved Study Quality Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] [[B2AI_TOPIC:1]](DataTopic.markdown) Human biospecimens are subject to a number of different collection, processing, and storage factors that can significantly alter their molecular composition and consistency. These biospecimen preanalytical factors, in turn, influence experimental outcomes and the ability to reproduce scientific results. Currently, the extent and type of information specific to the biospecimen preanalytical conditions reported in scientific publications and regulatory submissions varies widely. To improve the quality of research utilizing human tissues, it is critical that information regarding the handling of biospecimens be reported in a thorough, accurate, and standardized manner. The Biospecimen Reporting for Improved Study Quality (BRISQ) recommendations outlined herein are intended to apply to any study in which human biospecimens are used. The purpose of reporting these details is to supply others, from researchers to regulators, with more consistent and standardized information to better evaluate, interpret, compare, and reproduce the experimental results. The BRISQ guidelines are proposed as an important and timely resource tool to strengthen communication and publications around biospecimen-related research and help reassure patient contributors and the advocacy community that the contributions are valued and respected True False [[B2AI_ORG:72]](Organization.markdown) doi:10.1002/cncy.20147 -[B2AI_STANDARD:32](DataStandardOrTool.markdown) BiomedicalStandard BioXSD BioXSD Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:20]](DataTopic.markdown) Data model and exchange formats for basic bioinformatics types of data - sequences, alignments, feature records with associated data and metadata. True False http://bioxsd.org/ https://github.com/bioxsd/bioxsd [[B2AI_ORG:28]](Organization.markdown) doi:10.1093/bioinformatics/btq391 -[B2AI_STANDARD:33](DataStandardOrTool.markdown) BiomedicalStandard BIDS Brain Imaging Data Structure Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:22]](DataTopic.markdown) The Brain Imaging Data Structure (BIDS) is a simple and intuitive way to organize and describe data. This document defines the BIDS specification, which provides many details to help implement the standard. It includes the core specification as well as many extensions to specific brain imaging modalities, and increasingly also to other kinds of data. True False https://bids-specification.readthedocs.io/en/stable/ https://github.com/bids-standard/bids-specification doi:10.1038/sdata.2016.44 +[B2AI_STANDARD:32](DataStandardOrTool.markdown) BiomedicalStandard BioXSD BioXSD Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:20]](DataTopic.markdown) Data model and exchange formats for basic bioinformatics types of data - sequences, alignments, feature records with associated data and metadata. True False http://bioxsd.org/ https://github.com/bioxsd/bioxsd [[B2AI_ORG:28]](Organization.markdown) doi:10.1093/bioinformatics/btq391 +[B2AI_STANDARD:33](DataStandardOrTool.markdown) BiomedicalStandard BIDS Brain Imaging Data Structure Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:22]](DataTopic.markdown) The Brain Imaging Data Structure (BIDS) is a simple and intuitive way to organize and describe data. This document defines the BIDS specification, which provides many details to help implement the standard. It includes the core specification as well as many extensions to specific brain imaging modalities, and increasingly also to other kinds of data. True False https://bids-specification.readthedocs.io/en/stable/ https://github.com/bids-standard/bids-specification doi:10.1038/sdata.2016.44 [B2AI_STANDARD:34](DataStandardOrTool.markdown) BiomedicalStandard BFI Brief Fatigue Inventory Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [diagnosticinstrument] [[B2AI_TOPIC:9]](DataTopic.markdown) The Brief Fatigue Inventory (BFI) is used to rapidly assess the severity and impact of cancer-related fatigue. An increasing focus on cancer-related fatigue emphasized the need for sensitive tools to assess this most frequently reported symptom. The six interference items correlate with standard quality-of-life measures. True False https://www.mdanderson.org/research/departments-labs-institutes/departments-divisions/symptom-research/symptom-assessment-tools/brief-fatigue-inventory.html http://www.npcrc.org/files/news/brief_fatigue_inventory.pdf doi:10.1002/(sici)1097-0142(19990301)85:5<1186::aid-cncr24>3.0.co;2-n [B2AI_STANDARD:35](DataStandardOrTool.markdown) BiomedicalStandard BPI Brief Pain Inventory Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [diagnosticinstrument] [[B2AI_TOPIC:9]](DataTopic.markdown) The Brief Pain Inventory (BPI) rapidly assesses the severity of pain and its impact on functioning. The BPI has been translated into dozens of languages, and it is widely used in both research and clinical settings. True False https://www.mdanderson.org/research/departments-labs-institutes/departments-divisions/symptom-research/symptom-assessment-tools/brief-pain-inventory.html http://www.npcrc.org/files/news/briefpain_short.pdf [B2AI_STANDARD:36](DataStandardOrTool.markdown) BiomedicalStandard BED Browser Extensible Data Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) BED (Browser Extensible Data) format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required fields and nine additional optional fields. The number of fields per line must be consistent throughout any single set of data in an annotation track. The order of the optional fields is binding. Lower-numbered fields must always be populated if higher-numbered fields are used. True False https://genome.ucsc.edu/FAQ/FAQformat.html#format1 https://github.com/samtools/hts-specs/blob/master/BEDv1.pdf @@ -45,8 +45,8 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:44](DataStandardOrTool.markdown) BiomedicalStandard SDTM CDISC Controlled Terminology Standards for Data Aggregation through Study Data Tabulation Model (including QRS, Medical Device and Pharmacogenomics Data) Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4]](DataTopic.markdown) A standard for organizing and formatting data to streamline processes in collection, management, analysis and reporting. True False https://www.cdisc.org/standards/foundational/sdtm https://evs.nci.nih.gov/ftp1/CDISC/SDTM/ [[B2AI_ORG:15]](Organization.markdown) [B2AI_STANDARD:45](DataStandardOrTool.markdown) BiomedicalStandard CDASH CDISC Controlled Terminology Standards for Data Collection through Clinical Data Acquisition Standards Harmonization Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4]](DataTopic.markdown) A standard way to collect data consistently across studies and sponsors so that data collection formats and structures provide clear traceability of submission data into the Study Data Tabulation Model (SDTM). True False https://www.cdisc.org/standards/foundational/cdash https://evs.nci.nih.gov/ftp1/CDISC/SDTM/ [[B2AI_ORG:15]](Organization.markdown) [B2AI_STANDARD:46](DataStandardOrTool.markdown) BiomedicalStandard CDISC Dataset CDISC Dataset-XML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] CDISC Dataset-XML, which was released for comment under the name “StudyDataSet-XML” but was renamed to avoid confusion with the CDISC SDS team, is a new standard used to exchange study datasets in an XML format. The purpose of Dataset-XML is to support the interchange of tabular data for clinical research applications using ODM-based XML technologies. The Dataset-XML model is based on the CDISC Operational Data Model (ODM) standard and should follow the metadata structure defined in the CDISC Define-XML standard. Dataset-XML can represent any tabular dataset including SDTM, ADaM, SEND, or non-standard legacy datasets. Some noteworthy items relating to Dataset-XML v1.0 include alternative to SAS Version 5 Transport (XPT) format for datasets ODM-based model for representation of SEND, SDTM, ADaM or legacy datasets Capable of supporting CDISC regulatory data submissions Based on Define-XML v2 or v1 metadata, easy to reference Dataset-XML supports all language encodings supported by XML. True True https://www.cdisc.org/standards/data-exchange/dataset-xml [[B2AI_ORG:15]](Organization.markdown) -[B2AI_STANDARD:47](DataStandardOrTool.markdown) BiomedicalStandard CDISC LAB CDISC Laboratory Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:4]](DataTopic.markdown) LAB provides a standard model for the acquisition and exchange of laboratory data, primarily between labs and sponsors or CROs. The LAB standard was specifically designed for the interchange of lab data acquired in clinical trials. True True https://www.cdisc.org/standards/data-exchange/lab [[B2AI_ORG:15]](Organization.markdown) -[B2AI_STANDARD:48](DataStandardOrTool.markdown) BiomedicalStandard CDISC ODM CDISC Operational Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:4]](DataTopic.markdown) standard for exchanging biomedical data True False https://www.cdisc.org/standards/data-exchange/odm [[B2AI_ORG:15]](Organization.markdown) +[B2AI_STANDARD:47](DataStandardOrTool.markdown) BiomedicalStandard CDISC LAB CDISC Laboratory Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:4]](DataTopic.markdown) LAB provides a standard model for the acquisition and exchange of laboratory data, primarily between labs and sponsors or CROs. The LAB standard was specifically designed for the interchange of lab data acquired in clinical trials. True True https://www.cdisc.org/standards/data-exchange/lab [[B2AI_ORG:15]](Organization.markdown) +[B2AI_STANDARD:48](DataStandardOrTool.markdown) BiomedicalStandard CDISC ODM CDISC Operational Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:4]](DataTopic.markdown) standard for exchanging biomedical data True False https://www.cdisc.org/standards/data-exchange/odm [[B2AI_ORG:15]](Organization.markdown) [B2AI_STANDARD:49](DataStandardOrTool.markdown) BiomedicalStandard CDISC PRM CDISC Protocol Representation Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4]](DataTopic.markdown) The CDISC Protocol Representation Model Version 1.0 (PRM V1.0) is intended for those involved in the planning and design of a research protocol. The model focuses on the characteristics of a study and the definition and association of activities within the protocols, including arms and epochs. PRM V1.0 also includes the definitions of the roles that participate in those activities. The scope of this model includes protocol content including Study Design, Eligibility Criteria, and the requirements from the ClinicalTrials.gov and World Health Organization (WHO) registries. The majority of business requirements were provided by subject matter experts in clinical trial protocols. PRM V1.0 is based on the BRIDG Release 3.0 Protocol Representation sub-domain. It includes all classes in the BRIDG Protocol Representation sub-domain plus some classes from other BRIDG sub-domains, generally classes required for ClinicalTrials.gov and the WHO registries. True True https://www.cdisc.org/standards/foundational/protocol [[B2AI_ORG:15]](Organization.markdown) [B2AI_STANDARD:50](DataStandardOrTool.markdown) BiomedicalStandard SEND CDISC Standard for the Exchange of Nonclinical Data Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 The CDISC SEND is intended to guide the organization, structure, and format of standard nonclinical tabulation datasets for interchange between organizations such as sponsors and CROs and for submission to the US Food and Drug Administration (FDA) True True https://www.cdisc.org/standards/foundational/send [[B2AI_ORG:15]](Organization.markdown) [B2AI_STANDARD:51](DataStandardOrTool.markdown) BiomedicalStandard CDISC SDM CDISC Study Design Model in XML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4]](DataTopic.markdown) The CDISC Study Design Model in XML (SDM-XML) version 1.0 allows organizations to provide rigorous, machine-readable, interchangeable descriptions of the designs of their clinical studies, including treatment plans, eligibility and times and events. As an extension to the existing CDISC Operational Data Model (ODM) specification, SDM-XML affords implementers the ease of leveraging existing ODM concepts and re-using existing ODM definitions. SDM-XML defines three key sub-modules – Structure, Workflow, and Timing – permitting various levels of detail in any representation of a clinical study’s design, while allowing a high degree of authoring flexibility. The specification document is available for download as a PDF file. A ZIP file containing the XML Schemas, several examples, and an SDM-XML element and attribute reference also is available. True True https://www.cdisc.org/standards/data-exchange/sdm-xml [[B2AI_ORG:15]](Organization.markdown) @@ -54,14 +54,14 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:53](DataStandardOrTool.markdown) BiomedicalStandard chain Chain Format for pairwise alignment Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) The chain format describes a pairwise alignment that allow gaps in both sequences simultaneously. True False http://genome.ucsc.edu/goldenPath/help/chain.html [B2AI_STANDARD:54](DataStandardOrTool.markdown) BiomedicalStandard CARD CHARMM Card File Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:27]](DataTopic.markdown) The CARD file format is the standard means in CHARMM for providing a human readable and writable coordinate file. True False https://charmm-gui.org/charmmdoc/io.html [B2AI_STANDARD:55](DataStandardOrTool.markdown) BiomedicalStandard CML Chemical Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:3]](DataTopic.markdown) CML (Chemical Markup Language) is an XML language designed to hold most of the central concepts in chemistry. It was the first language to be developed and plays the same role for chemistry as MathML for mathematics and GML for geographical systems. CML covers most mainstream chemistry and especially molecules, reactions, solid-state, computation and spectroscopy. Since it has a special flexible approach to numeric science it also covers a very wide range of chemical properties, parameters and experimental observation. It is particularly concerned with the communication between machines and humans, and machines to machines. It has been heavily informed by the current chemical scholarly literature and chemical databases. XML is a mainstream approach providing semantics for science, such as MathML, SBML/BIOPAX (biology), GML and KML (geo) SVG (graphics) and NLM-DTD, ODT and OOXML (documents). CML provides support for most chemistry, especially molecules, compounds, reactions, spectra, crystals and computational chemistry (compchem). CML has been developed by Peter Murray-Rust and Henry Rzepa since 1995. It is the de facto XML for chemistry, accepted by publishers and with more than 1 million lines of Open Source code supporting it. CML can be validated and built into authoring tools (for example the Chemistry Add-in for Microsoft Word). A list of CML-compliant and CML-aware software can be found on the software page. The infrastructure includes legacy converters, dictionaries and conventions, Semantic Web and Linked Open Data. There are several versions of the CML schema. The most recent schema is schema 3. This essentially relaxes many of the constraints imposed in the previous stable release (schema 2.4), allowing users to put together the elements and attributes in a more flexible manner to fit the data that they want to represent more easily. True False https://www.xml-cml.org/ -[B2AI_STANDARD:56](DataStandardOrTool.markdown) BiomedicalStandard ClinGen Interpretation ClinGen Interpretation Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:4|B2AI_TOPIC:35]](DataTopic.markdown) Provides a structure and format for exchanging information about the clinical effect of genetic variants, which retains the contextual and supporting information related to the interpretation of the variant. True False https://dataexchange.clinicalgenome.org/interpretation/ https://github.com/clingen-data-model/clingen-interpretation +[B2AI_STANDARD:56](DataStandardOrTool.markdown) BiomedicalStandard ClinGen Interpretation ClinGen Interpretation Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:4|B2AI_TOPIC:35]](DataTopic.markdown) Provides a structure and format for exchanging information about the clinical effect of genetic variants, which retains the contextual and supporting information related to the interpretation of the variant. True False https://dataexchange.clinicalgenome.org/interpretation/ https://github.com/clingen-data-model/clingen-interpretation [B2AI_STANDARD:57](DataStandardOrTool.markdown) BiomedicalStandard CLSI AUTO16 CLSI Next-Generation In Vitro Diagnostic Interface Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 Exchange of data about and produced by in vitro diagnostic tests. False True https://clsi.org/standards/products/automation-and-informatics/documents/auto16/ [[B2AI_ORG:16]](Organization.markdown) [B2AI_STANDARD:58](DataStandardOrTool.markdown) BiomedicalStandard MSF CLUSTAL-W Alignment Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13|B2AI_TOPIC:26|B2AI_TOPIC:28]](DataTopic.markdown) Format for a multiple alignment of protein or DNA sequences. True False https://bioinfo.nhri.edu.tw/gcg/doc/11.0/clustalw+.html [B2AI_STANDARD:59](DataStandardOrTool.markdown) BiomedicalStandard DND CLUSTAL-W Dendrogram Guide File Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:12|B2AI_TOPIC:13|B2AI_TOPIC:26|B2AI_TOPIC:28]](DataTopic.markdown) Format for the tree (or “dendrogram”) used to guide the a multiple sequence alignment process. True False https://bioinfo.nhri.edu.tw/gcg/doc/11.0/clustalw+.html [B2AI_STANDARD:60](DataStandardOrTool.markdown) BiomedicalStandard CODE-EHR CODE-EHR best-practice framework for the use of structured electronic health-care records in clinical research Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] [[B2AI_TOPIC:9]](DataTopic.markdown) ...we propose the CODE-EHR minimum standards framework to be used by researchers and clinicians to improve the design of studies and enhance transparency of study methods. The CODE-EHR framework aims to develop robust and effective utilisation of health-care data for research purposes. True False doi:10.1016/S2589-7500(22)00151-0 [B2AI_STANDARD:61](DataStandardOrTool.markdown) BiomedicalStandard CXI Coherent X-ray Imaging Data Bank format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:15]](DataTopic.markdown) The CXI format was created as common format for all the data in the Coherent X-ray Imaging Data Bank (CXIDB). Naturally its scope is all experimental data collected during Coherent X-ray Imaging experiments as well as all data generated during the analysis of the experimental data. True False https://www.cxidb.org/cxi.html -[B2AI_STANDARD:62](DataStandardOrTool.markdown) BiomedicalStandard CCPN Collaborative Computing Project for the NMR community data model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:5]](DataTopic.markdown) The CCPN Data Model for macromolecular NMR is intended to cover all data needed for macromolecular NMR spectroscopy from the initial experimental data to the final validation. It serves for exchange of data between programs, for storage, data harvesting, and database deposition. The data model proper is an abstract description of the relevant data and their relationships - it is implemented in the modeling language UML. From this CCPN autogenerates interfaces (APIs) for various languages, format description and I/O routines, and documentation. True False https://sites.google.com/site/ccpnwiki/home/documentation/ccpnmr-analysis/core-concepts/the-ccpn-data-model doi:10.1002/prot.20449 -[B2AI_STANDARD:63](DataStandardOrTool.markdown) BiomedicalStandard CFDE C2M2 Common Fund Data Ecosystem Crosscut Metadata Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:5]](DataTopic.markdown) Biomedical metadata. True False https://docs.nih-cfde.org/en/latest/c2m2/draft-C2M2_specification/ https://osf.io/bq6k9/ [[B2AI_ORG:68]](Organization.markdown) +[B2AI_STANDARD:62](DataStandardOrTool.markdown) BiomedicalStandard CCPN Collaborative Computing Project for the NMR community data model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) The CCPN Data Model for macromolecular NMR is intended to cover all data needed for macromolecular NMR spectroscopy from the initial experimental data to the final validation. It serves for exchange of data between programs, for storage, data harvesting, and database deposition. The data model proper is an abstract description of the relevant data and their relationships - it is implemented in the modeling language UML. From this CCPN autogenerates interfaces (APIs) for various languages, format description and I/O routines, and documentation. True False https://sites.google.com/site/ccpnwiki/home/documentation/ccpnmr-analysis/core-concepts/the-ccpn-data-model doi:10.1002/prot.20449 +[B2AI_STANDARD:63](DataStandardOrTool.markdown) BiomedicalStandard CFDE C2M2 Common Fund Data Ecosystem Crosscut Metadata Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) Biomedical metadata. True False https://docs.nih-cfde.org/en/latest/c2m2/draft-C2M2_specification/ https://osf.io/bq6k9/ [[B2AI_ORG:68]](Organization.markdown) [B2AI_STANDARD:64](DataStandardOrTool.markdown) BiomedicalStandard Common Metadata Common Metadata Elements for Cataloging Biomedical Datasets Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] This dataset outlines a proposed set of core, minimal metadata elements that can be used to describe biomedical datasets, such as those resulting from research funded by the National Institutes of Health. It can inform efforts to better catalog or index such data to improve discoverability. The proposed metadata elements are based on an analysis of the metadata schemas used in a set of NIH-supported data sharing repositories. Common elements from these data repositories were identified, mapped to existing data-specific metadata standards from to existing multidisciplinary data repositories, DataCite and Dryad, and compared with metadata used in MEDLINE records to establish a sustainable and integrated metadata schema. True False https://figshare.com/articles/dataset/Common_Metadata_Elements_for_Cataloging_Biomedical_Datasets/1496573 https://figshare.com/articles/dataset/Common_Metadata_Elements_for_Cataloging_Biomedical_Datasets/1496573?file=3377663 [B2AI_STANDARD:65](DataStandardOrTool.markdown) BiomedicalStandard FACIT-COST COmprehensive Score for financial Toxicity A FACIT Measure of Financial Toxicity Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [diagnosticinstrument] Developed in conjunction with the University of Chicago, the COST is a patient-reported outcome measure that describes the financial distress experienced by cancer patients. Since its initial publication, an additional item from the FACIT System has been included to screen for financial toxicity and to provide a good global summary item for financial toxicity. True False https://www.facit.org/measures/FACIT-COST [[B2AI_ORG:30]](Organization.markdown) doi:10.1002/cncr.30369 [B2AI_STANDARD:66](DataStandardOrTool.markdown) BiomedicalStandard C-CDA Consolidated Clinical Document Architecture Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:9]](DataTopic.markdown) A widely-used, XML-based format for electronic health records. Superceded by FHIR document standards. True True https://www.healthit.gov/topic/standards-technology/consolidated-cda-overview http://www.hl7.org/implement/standards/product_brief.cfm?product_id=492 [[B2AI_ORG:40]](Organization.markdown) @@ -77,26 +77,26 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:76](DataStandardOrTool.markdown) BiomedicalStandard DOS-DP Dead simple owl design pattern exchange format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) A simple design pattern system that can easily be consumed, whatever your code base, for OWL ontologies. True False https://oboacademy.github.io/obook/tutorial/dosdp-template/ https://github.com/INCATools/dead_simple_owl_design_patterns [[B2AI_ORG:58]](Organization.markdown) doi:10.1186/s13326-017-0126-0 [B2AI_STANDARD:77](DataStandardOrTool.markdown) BiomedicalStandard DMN Decision Model and Notation Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) A modeling language and notation for the precise specification of business decisions and business rules. True False https://www.omg.org/dmn/ [[B2AI_ORG:10]](Organization.markdown) [B2AI_STANDARD:78](DataStandardOrTool.markdown) BiomedicalStandard DELTA Description Language for Taxonomy Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:5]](DataTopic.markdown) When taxonomic descriptions are prepared for input to computer programs, the form of the coding is usually dictated by the requirements of a particular program or set of programs. This restricts the type of data that can be represented, and the number of other programs that can use the data. Even when working with a particular program, it is frequently necessary to set up different versions of the same basic data, for example, when using restricted sets of taxa or characters to make special-purpose keys. The potential advantages of automation, especially in connexion with large groups, cannot be realized if the data have to be restructured by hand for every operation. The DELTA (DEscription Language for TAxonomy) system was developed to overcome these problems. It was designed primarily for easy use by people rather than for convenience in computer programming, and is versatile enough to replace the written description as the primary means of recording data. Consequently, it can be used as a shorthand method of recording data, even if computer processing of the data is not envisaged. True False https://www.delta-intkey.com/ -[B2AI_STANDARD:79](DataStandardOrTool.markdown) BiomedicalStandard DICOMDIR DICOM Part 10 Media Storage and File Format for Media Interchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [audiovisual|fileformat] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies a general model for the storage of Medical Imaging information on removable media. The purpose of this Part is to provide a framework allowing the interchange of various types of medical images and related information on a broad range of physical storage media. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part10.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:79](DataStandardOrTool.markdown) BiomedicalStandard DICOMDIR DICOM Part 10 Media Storage and File Format for Media Interchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [audiovisual|fileformat|has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies a general model for the storage of Medical Imaging information on removable media. The purpose of this Part is to provide a framework allowing the interchange of various types of medical images and related information on a broad range of physical storage media. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part10.html [[B2AI_ORG:25]](Organization.markdown) [B2AI_STANDARD:80](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 11 DICOM Part 11 Media Storage Application Profiles Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies application specific subsets of the DICOM Standard to which an implementation may claim conformance. Such a conformance statement applies to the interoperable interchange of medical images and related information on storage media for specific clinical uses. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part11.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:81](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 12 DICOM Part 12 Media Formats and Physical Media for Media Interchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard facilitates the interchange of information between digital imaging computer systems in medical environments. This interchange will enhance diagnostic imaging and potentially other clinical applications. The multi-part DICOM Standard defines the services and data that shall be supplied to achieve this interchange of information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part12.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:82](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 14 DICOM Part 14 Grayscale Standard Display Function Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) PS3.14 specifies a standardized Display Function for display of grayscale images. It provides examples of methods for measuring the Characteristic Curve of a particular Display System for the purpose of either altering the Display System to match the Grayscale Standard Display Function, or for measuring the conformance of a Display System to the Grayscale Standard Display Function. Display Systems include such things as monitors with their associated driving electronics and printers producing films that are placed on light-boxes or alternators. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part14.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:83](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 15 DICOM Part 15 Security and System Management Profiles Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies Security and System Management Profiles to which implementations may claim conformance. Security and System Management Profiles are defined by referencing externally developed standard protocols, such as TLS, ISCL, DHCP, and LDAP, with attention to their use in a system that uses DICOM Standard protocols for information interchange. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part15.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:84](DataStandardOrTool.markdown) BiomedicalStandard DCMR DICOM Part 16 Content Mapping Resource Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies the DICOM Content Mapping Resource (DCMR), which defines the Templates and Context Groups used elsewhere in the Standard. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part16.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:85](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 17 DICOM Part 17 Explanatory Information Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard contains explanatory information in the form of Normative and Informative Annexes. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part17.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:86](DataStandardOrTool.markdown) BiomedicalStandard DICOMweb DICOM Part 18 Web Services Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) PS3.18 specifies web services (using the HTTP family of protocols) for managing and distributing DICOM (Digital Imaging and Communications in Medicine) Information Objects, such as medical images, annotations, reports, etc. to healthcare organizations, providers, and patients. The term DICOMweb is used to designate the RESTful Web Services described here. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part18.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:87](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 19 DICOM Part 19 Application Hosting Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard defines an interface between two software applications. One application, the Hosting System, provides the second application with data, such as a set of images and related data. The second application, the Hosted Application, analyzes that data, potentially returning the results of that analysis, for example in the form of another set of images and/or structured reports, to the first application. Such an Application Program Interface (API) differs in scope from other portions of the DICOM Standard in that it standardizes the data interchange between software components on the same system, instead of data interchange between different systems. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part19.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:88](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 2 DICOM Part 2 Conformance Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) An implementation need not employ all the optional components of the DICOM Standard. After meeting the minimum general requirements, a conformant DICOM implementation may utilize whatever SOP Classes, communications protocols, Media Storage Application Profiles, optional (Type 3) Attributes, codes and controlled terminology, etc., needed to accomplish its designed task. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part02.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:89](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 20 DICOM Part 20 Imaging Reports using HL7 Clinical Document Architecture Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies templates for the encoding of imaging reports using the HL7 Clinical Document Architecture Release 2 (CDA R2, or simply CDA) Standard. Within this scope are clinical procedure reports for specialties that use imaging for screening, diagnostic, or therapeutic purposes. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part20.html [[B2AI_ORG:25|B2AI_ORG:40]](Organization.markdown) -[B2AI_STANDARD:90](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 21 DICOM Part 21 Transformations between DICOM and other Representations Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies the transformations between DICOM and other representations of the same information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part21.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:91](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 22 DICOM Part 22 Real-Time Communication Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies an SMPTE ST 2110-10 based service, relying on RTP, for the real-time transport of DICOM metadata. It provides a mechanism for the transport of DICOM metadata associated with a video or an audio flow based on the SMPTE ST 2110-20 and SMPTE ST 2110-30, respectively. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part22.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:92](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 3 DICOM Part 3 Information Object Definitions Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies the set of Information Object Definitions (IODs) that provide an abstract definition of real-world objects applicable to communication of digital medical information. For each IOD, this Part specifies any necessary information for the semantic description of the IOD, relationships to associated real-world objects relevant to the IOD, Attributes that describe the characteristics of the IOD. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part03.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:93](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 4 DICOM Part 4 Service Class Specifications Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies the set of Service Class Definitions that provide an abstract definition of real-world activities applicable to communication of digital medical information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part04.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:94](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 5 DICOM Part 5 Data Structures and Encoding Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) In this Part of the Standard the structure and encoding of the Data Set is specified. In the context of Application Entities communicating over a network, a Data Set is that portion of a DICOM Message that conveys information about real world objects being managed over the network. A Data Set may have other contexts in other applications of this Standard; e.g., in media exchange the Data Set translates to file content structure. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part05.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:95](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 6 DICOM Part 6 Data Dictionary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard is PS 3.6 of a multi-part standard produced to facilitate the interchange of information between digital imaging computer systems in medical environments. This interchange will enhance diagnostic imaging and potentially other clinical applications. The multi-part DICOM Standard covers the protocols and data that shall be supplied to achieve this interchange of information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part06.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:96](DataStandardOrTool.markdown) BiomedicalStandard DIMSE DICOM Part 7 Message Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies the DICOM Message Service Element (DIMSE). The DIMSE defines an Application Service Element (both the service and protocol) used by peer DICOM Application Entities for the purpose of exchanging medical images and related information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part07.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:97](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 8 DICOM Part 8 Network Communication Support for Message Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) The Communication Protocols specified in this Part of PS3 closely fit the ISO Open Systems Interconnection Basic Reference Model (ISO 7498-1, see Figure 1-1). They relate to the following layers - Physical, Data Link, Network, Transport, Session, Presentation and the Association Control Services (ACSE) of the Application layer. The communication protocols specified by this Part are general purpose communication protocols (TCP/IP) and not specific to this Standard. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part08.html [[B2AI_ORG:25]](Organization.markdown) -[B2AI_STANDARD:98](DataStandardOrTool.markdown) BiomedicalStandard DICOM Digital Imaging And Communications In Medicine Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) Radiology imaging, including templates for narrative reports and machine-generated output. True False https://www.dicomstandard.org/ https://www.dicomstandard.org/current [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:81](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 12 DICOM Part 12 Media Formats and Physical Media for Media Interchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard facilitates the interchange of information between digital imaging computer systems in medical environments. This interchange will enhance diagnostic imaging and potentially other clinical applications. The multi-part DICOM Standard defines the services and data that shall be supplied to achieve this interchange of information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part12.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:82](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 14 DICOM Part 14 Grayscale Standard Display Function Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) PS3.14 specifies a standardized Display Function for display of grayscale images. It provides examples of methods for measuring the Characteristic Curve of a particular Display System for the purpose of either altering the Display System to match the Grayscale Standard Display Function, or for measuring the conformance of a Display System to the Grayscale Standard Display Function. Display Systems include such things as monitors with their associated driving electronics and printers producing films that are placed on light-boxes or alternators. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part14.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:83](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 15 DICOM Part 15 Security and System Management Profiles Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies Security and System Management Profiles to which implementations may claim conformance. Security and System Management Profiles are defined by referencing externally developed standard protocols, such as TLS, ISCL, DHCP, and LDAP, with attention to their use in a system that uses DICOM Standard protocols for information interchange. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part15.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:84](DataStandardOrTool.markdown) BiomedicalStandard DCMR DICOM Part 16 Content Mapping Resource Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies the DICOM Content Mapping Resource (DCMR), which defines the Templates and Context Groups used elsewhere in the Standard. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part16.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:85](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 17 DICOM Part 17 Explanatory Information Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard contains explanatory information in the form of Normative and Informative Annexes. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part17.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:86](DataStandardOrTool.markdown) BiomedicalStandard DICOMweb DICOM Part 18 Web Services Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) PS3.18 specifies web services (using the HTTP family of protocols) for managing and distributing DICOM (Digital Imaging and Communications in Medicine) Information Objects, such as medical images, annotations, reports, etc. to healthcare organizations, providers, and patients. The term DICOMweb is used to designate the RESTful Web Services described here. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part18.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:87](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 19 DICOM Part 19 Application Hosting Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard defines an interface between two software applications. One application, the Hosting System, provides the second application with data, such as a set of images and related data. The second application, the Hosted Application, analyzes that data, potentially returning the results of that analysis, for example in the form of another set of images and/or structured reports, to the first application. Such an Application Program Interface (API) differs in scope from other portions of the DICOM Standard in that it standardizes the data interchange between software components on the same system, instead of data interchange between different systems. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part19.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:88](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 2 DICOM Part 2 Conformance Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) An implementation need not employ all the optional components of the DICOM Standard. After meeting the minimum general requirements, a conformant DICOM implementation may utilize whatever SOP Classes, communications protocols, Media Storage Application Profiles, optional (Type 3) Attributes, codes and controlled terminology, etc., needed to accomplish its designed task. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part02.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:89](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 20 DICOM Part 20 Imaging Reports using HL7 Clinical Document Architecture Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies templates for the encoding of imaging reports using the HL7 Clinical Document Architecture Release 2 (CDA R2, or simply CDA) Standard. Within this scope are clinical procedure reports for specialties that use imaging for screening, diagnostic, or therapeutic purposes. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part20.html [[B2AI_ORG:25|B2AI_ORG:40]](Organization.markdown) +[B2AI_STANDARD:90](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 21 DICOM Part 21 Transformations between DICOM and other Representations Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies the transformations between DICOM and other representations of the same information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part21.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:91](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 22 DICOM Part 22 Real-Time Communication Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies an SMPTE ST 2110-10 based service, relying on RTP, for the real-time transport of DICOM metadata. It provides a mechanism for the transport of DICOM metadata associated with a video or an audio flow based on the SMPTE ST 2110-20 and SMPTE ST 2110-30, respectively. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part22.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:92](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 3 DICOM Part 3 Information Object Definitions Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies the set of Information Object Definitions (IODs) that provide an abstract definition of real-world objects applicable to communication of digital medical information. For each IOD, this Part specifies any necessary information for the semantic description of the IOD, relationships to associated real-world objects relevant to the IOD, Attributes that describe the characteristics of the IOD. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part03.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:93](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 4 DICOM Part 4 Service Class Specifications Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies the set of Service Class Definitions that provide an abstract definition of real-world activities applicable to communication of digital medical information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part04.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:94](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 5 DICOM Part 5 Data Structures and Encoding Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) In this Part of the Standard the structure and encoding of the Data Set is specified. In the context of Application Entities communicating over a network, a Data Set is that portion of a DICOM Message that conveys information about real world objects being managed over the network. A Data Set may have other contexts in other applications of this Standard; e.g., in media exchange the Data Set translates to file content structure. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part05.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:95](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 6 DICOM Part 6 Data Dictionary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard is PS 3.6 of a multi-part standard produced to facilitate the interchange of information between digital imaging computer systems in medical environments. This interchange will enhance diagnostic imaging and potentially other clinical applications. The multi-part DICOM Standard covers the protocols and data that shall be supplied to achieve this interchange of information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part06.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:96](DataStandardOrTool.markdown) BiomedicalStandard DIMSE DICOM Part 7 Message Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) This Part of the DICOM Standard specifies the DICOM Message Service Element (DIMSE). The DIMSE defines an Application Service Element (both the service and protocol) used by peer DICOM Application Entities for the purpose of exchanging medical images and related information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part07.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:97](DataStandardOrTool.markdown) BiomedicalStandard DICOM Part 8 DICOM Part 8 Network Communication Support for Message Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) The Communication Protocols specified in this Part of PS3 closely fit the ISO Open Systems Interconnection Basic Reference Model (ISO 7498-1, see Figure 1-1). They relate to the following layers - Physical, Data Link, Network, Transport, Session, Presentation and the Association Control Services (ACSE) of the Application layer. The communication protocols specified by this Part are general purpose communication protocols (TCP/IP) and not specific to this Standard. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part08.html [[B2AI_ORG:25]](Organization.markdown) +[B2AI_STANDARD:98](DataStandardOrTool.markdown) BiomedicalStandard DICOM Digital Imaging And Communications In Medicine Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) Radiology imaging, including templates for narrative reports and machine-generated output. True False https://www.dicomstandard.org/ https://www.dicomstandard.org/current [[B2AI_ORG:25]](Organization.markdown) [B2AI_STANDARD:99](DataStandardOrTool.markdown) BiomedicalStandard Direct Standard Direct Applicability Statement for Secure Health Transport Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 Describes how to use SMTP, S/MIME, and X.509 certificates to securely transport health information over the Internet. True False https://wiki.directproject.org/w/images/e/e6/Applicability_Statement_for_Secure_Health_Transport_v1.2.pdf [[B2AI_ORG:26]](Organization.markdown) [B2AI_STANDARD:100](DataStandardOrTool.markdown) BiomedicalStandard DAS Distributed Sequence Annotation System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:12|B2AI_TOPIC:13]](DataTopic.markdown) Allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. True False https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-2-7/MediaObjects/12859_2001_8_MOESM1_ESM.pdf doi:10.1186/1471-2105-2-7 [B2AI_STANDARD:101](DataStandardOrTool.markdown) BiomedicalStandard EML Ecological Metadata Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] A metadata standard developed for the earth, environmental and ecological sciences. True False https://eml.ecoinformatics.org/ doi:10.5063/F11834T2 @@ -126,7 +126,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:125](DataStandardOrTool.markdown) BiomedicalStandard FANLTC Functional Assessment of Non-Life Threatening Conditions Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [diagnosticinstrument] [[B2AI_TOPIC:9]](DataTopic.markdown) The Functional Assessment of Non-Life Threatening Conditions (FANLTC) is a 26-item version of the FACT-G designed to be administered to patients with non-life threatening conditions. The item from the FACT-G making reference to anxiety about death has been removed, and the instrument measures four domains of HRQOL - Physical, social/family, emotional and functional well-being. True False https://www.facit.org/measures/FANLTC [[B2AI_ORG:30]](Organization.markdown) [B2AI_STANDARD:126](DataStandardOrTool.markdown) BiomedicalStandard Regier2018 Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:13|B2AI_TOPIC:35]](DataTopic.markdown) WGS data processing standards that allow different groups to produce functionally equivalent (FE) results, yet still innovate on data processing pipelines. True False https://github.com/CCDG/Pipeline-Standardization doi:10.1038/s41467-018-06159-4 [B2AI_STANDARD:127](DataStandardOrTool.markdown) BiomedicalStandard FuGE-ML Functional Genomics Experiment Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:13]](DataTopic.markdown) Functional genomics experiments present many challenges in data archiving, sharing and querying. As the size and complexity of data generated from such experiments grows, so does the requirement for standard data formats. To address these needs, the Functional Genomics Experiment [Object Model / Markup-Language] (FuGE-OM, FuGE-ML) has been created to facilitate the development of data standards.FuGE is a model of the shared components in different functional genomics domains. FuGE facilitates the development of data standards in functional genomics in two ways. 1. FuGE provides a model of common components in functional genomics investigations, such as materials, data, protocols, equipment and software. These models can be extended to develop modular data formats with consistent structure. 2. FuGE provides a framework for capturing complete laboratory workflows, enabling the integration of pre-existing data formats. In this context, FuGE allows the capture of additional metadata that gives formats a context within the complete workflow. FuGE is available as a UML model and an XML Schema True False https://fuge.sourceforge.net/index.php -[B2AI_STANDARD:128](DataStandardOrTool.markdown) BiomedicalStandard FuGEFlow Functional Genomics Experiment model for flow cytometry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:13]](DataTopic.markdown) FuGEFlow represents a collaborative effort to develop of flow cytometry experimental workflow description based on the FuGE model. The Functional Genomics Experiment data model (FuGE) describes common aspects of comprehensive, high-throughput experiments. FuGE is an extendable model that provides a basis for creation of new technology-specific data formats, such as FuGEFlow for flow cytometry. True False doi:10.1186/1471-2105-10-184 +[B2AI_STANDARD:128](DataStandardOrTool.markdown) BiomedicalStandard FuGEFlow Functional Genomics Experiment model for flow cytometry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:13]](DataTopic.markdown) FuGEFlow represents a collaborative effort to develop of flow cytometry experimental workflow description based on the FuGE model. The Functional Genomics Experiment data model (FuGE) describes common aspects of comprehensive, high-throughput experiments. FuGE is an extendable model that provides a basis for creation of new technology-specific data formats, such as FuGEFlow for flow cytometry. True False doi:10.1186/1471-2105-10-184 [B2AI_STANDARD:129](DataStandardOrTool.markdown) BiomedicalStandard FAF Functionality Assessment Flowchart Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [diagnosticinstrument] [[B2AI_TOPIC:9]](DataTopic.markdown) A method to measure performance status with a high percentage of agreement between observers. True False doi:10.1186/s12885-015-1526-0 [B2AI_STANDARD:130](DataStandardOrTool.markdown) BiomedicalStandard GA4GH GA4GH metadata model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:13]](DataTopic.markdown) The metadata model for GA4GH, an international coalition of both public and private interested parties, formed to enable the sharing of genomic and clinical data. True False https://github.com/ga4gh-metadata/metadata-schemas [[B2AI_ORG:34]](Organization.markdown) [B2AI_STANDARD:131](DataStandardOrTool.markdown) BiomedicalStandard Gating-ML Gating-ML specification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:5]](DataTopic.markdown) The Gating-ML specification represents a proposal on how to form unambiguous XML-based gate definitions that may be used independently as well as included as one of the components of ACS. Such a description of gates can facilitate the interchange and validation of data between different software packages with the potential of significant increase of hardware and software interoperability. The specification supports rectangular gates in n dimensions (i.e., from one-dimensional range gates up to n-dimensional hyper-rectangular regions), polygon gates in two (and more) dimensions, ellipsoid gates in n dimensions, decision tree structures, and Boolean collections of any of the types of gates. Gates can be uniquely identified and may be ordered into a hierarchical structure to describe a gating strategy. Gates may be applied on parameters as in list mode data files (e.g., FCS files) or on transformed parameters as described by any explicit parameter transformation. Therefore, since version 1.5, parameter transformation and compensation description are included as part of the Gating-ML specification. True False http://flowcyt.sourceforge.net/gating/ @@ -193,7 +193,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:192](DataStandardOrTool.markdown) BiomedicalStandard MSGISO Measuring Sex, Gender Identity, and Sexual Orientation Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] [[B2AI_TOPIC:6|B2AI_TOPIC:31]](DataTopic.markdown) Measuring Sex, Gender Identity, and Sexual Orientation recommends that the National Institutes of Health (NIH) adopt new practices for collecting data on sex, gender, and sexual orientation - including collecting gender data by default, and not conflating gender with sex as a biological variable. The report recommends standardized language to be used in survey questions that ask about a respondent's sex, gender identity, and sexual orientation. Better measurements will improve data quality, as well as the NIH's ability to identify LGBTQI+ populations and understand the challenges they face. True False https://nap.nationalacademies.org/catalog/26424/measuring-sex-gender-identity-and-sexual-orientation [[B2AI_ORG:60]](Organization.markdown) doi:10.17226/26424 [B2AI_STANDARD:193](DataStandardOrTool.markdown) BiomedicalStandard MNC Medical Imaging NetCDF (Minc) format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:22]](DataTopic.markdown) A system for flexible, self-documenting representation of neuroscientific imaging data with arbitrary orientation and dimensionality. True False https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/MINC2.0_File_Format_Reference doi:10.3389/fninf.2016.00035 [B2AI_STANDARD:194](DataStandardOrTool.markdown) BiomedicalStandard MS-DRG Medicare Severity Diagnosis Related Groups codes Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [codesystem] [[B2AI_TOPIC:9]](DataTopic.markdown) Medical cases in the US are classified into Medicare Severity Diagnosis Related Groups (MS-DRGs) for payment based on the following information reported by the hospital - the principal diagnosis, up to 24 additional diagnoses, and up to 25 procedures performed during the stay. In a small number of MS-DRGs, classification is also based on the age, sex, and discharge status of the patient. Effective October 1, 2015, the diagnosis and procedure information is reported by the hospital using codes from the International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) and the International Classification of Diseases, Tenth Revision, Procedure Coding System (ICD-10-PCS). True False https://www.cms.gov/Medicare/Medicare-Fee-for-Service-Payment/AcuteInpatientPPS/MS-DRG-Classifications-and-Software [[B2AI_ORG:17]](Organization.markdown) -[B2AI_STANDARD:195](DataStandardOrTool.markdown) BiomedicalStandard MEDIN MEDIN Discovery Metadata Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:11]](DataTopic.markdown) MEDIN is a list of information that accompanies a data set and allows other people to find out what the data set contains, where it was collected and how they can get hold of it. It is a standard for marine metadata and a set of tools to create metadata records that comply with the MEDIN Metadata Standard True False https://www.medin.org.uk/medin-discovery-metadata-standard https://github.com/medin-marine/Discovery-Standard-public-content +[B2AI_STANDARD:195](DataStandardOrTool.markdown) BiomedicalStandard MEDIN MEDIN Discovery Metadata Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:11]](DataTopic.markdown) MEDIN is a list of information that accompanies a data set and allows other people to find out what the data set contains, where it was collected and how they can get hold of it. It is a standard for marine metadata and a set of tools to create metadata records that comply with the MEDIN Metadata Standard True False https://www.medin.org.uk/medin-discovery-metadata-standard https://github.com/medin-marine/Discovery-Standard-public-content [B2AI_STANDARD:196](DataStandardOrTool.markdown) BiomedicalStandard MSAS Memorial Symptom Assessment Scale Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [diagnosticinstrument] [[B2AI_TOPIC:9]](DataTopic.markdown) The Memorial Symptom Assessment Scale (MSAS) is a new patient-rated instrument that was developed to provide multidimensional information about a diverse group of common symptoms. True False http://www.npcrc.org/files/news/memorial_symptom_assessment_scale.pdf doi:10.1016/0959-8049(94)90182-1 [B2AI_STANDARD:197](DataStandardOrTool.markdown) BiomedicalStandard MOD-CO Meta-omics Data and Collection Objects Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:13|B2AI_TOPIC:28|B2AI_TOPIC:34]](DataTopic.markdown) The conceptual and procedural meta-omics schema is developed as part of the MOD-CO project. It is entitled with MOD-CO schema, a conceptual schema for processing sample data in meta-omics research and published in various kind of schema representations. With that, the MOD-CO schema is a generic and comprehensive schema providing specifications useful for later software implementation and facilitates international standardisation processes. True False https://www.mod-co.net/wiki/Schema_Representations [B2AI_STANDARD:198](DataStandardOrTool.markdown) BiomedicalStandard MINiML MIAME Notation in Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] MINiML (MIAME Notation in Markup Language, pronounced 'minimal') is a data exchange format optimized for microarray gene expression data, as well as many other types of high-throughput molecular abundance data. MINiML assumes only very basic relations between objects - Platform (e.g., array), Sample (e.g., hybridization), and Series (experiment). MINiML captures all components of the MIAME checklist, as well as any additional information that the submitter wants to provide. MINiML uses XML Schema as syntax. True False https://www.ncbi.nlm.nih.gov/geo/info/MINiML.html [[B2AI_ORG:74]](Organization.markdown) @@ -226,11 +226,11 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:225](DataStandardOrTool.markdown) BiomedicalStandard NEMSIS National Emergency Medical Services Information System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 Standard for the collection and transmission of emergency medical services (EMS) operations and patient care data. True False https://nemsis.org/technical-resources/ [[B2AI_ORG:66]](Organization.markdown) [B2AI_STANDARD:226](DataStandardOrTool.markdown) BiomedicalStandard PCORNet CDM National Patient-Centered Clinical Research Network Common Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4]](DataTopic.markdown) This guiding principle is expressed in the CDM design through prioritization of analytic functionality, and a parsimonious approach based upon analytic utility. At times, this results in decisions that are not based in relational database modeling principles such as normalization. The model is designed to facilitate routine and rapid execution of distributed complex analytics. To meet this design requirement, some fields are duplicated across multiple tables to support faster analytic operations for distributed querying. The PCORnet CDM is based on the FDA Mini-Sentinel CDM. This allows PCORnet to more easily leverage the large array of analytic tools and expertise developed for the MSCDM v4.0, including data characterization approaches and the various tools for complex distributed analytics. True False http://pcornet.org/pcornet-common-data-model/ https://pcornet.org/wp-content/uploads/2022/01/PCORnet-Common-Data-Model-v60-2020_10_221.pdf [[B2AI_ORG:81]](Organization.markdown) [B2AI_STANDARD:227](DataStandardOrTool.markdown) BiomedicalStandard NCD Natural Collections Description standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 Natural Collections Description (NCD) (A data standard for exchanging data describing natural history collections) is a proposed data standard for describing collections of natural history materials at the collection level; one NCD record describes one entire collection. Collection descriptions are electronic records that document the holdings of an organisation as groups of items, which complement the more traditional item-level records such as are produced for a single specimen or a library book. NCD is tailored to natural history. It lies between general resource discovery standards such as Dublin Core (DC) and rich collection description standards such as the Encoded Archival Description (EAD). The NCD standard covers all types of natural history collections, such as specimens, original artwork, archives, observations, library materials, datasets, photographs or mixed collections such as those that result from expeditions and voyages of discovery. True False https://www.tdwg.org/standards/ncd/ [[B2AI_ORG:93]](Organization.markdown) -[B2AI_STANDARD:228](DataStandardOrTool.markdown) BiomedicalStandard BioProject Schema NCBI BioProject XML Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:1]](DataTopic.markdown) This is a XML Schema specification of BioProject data. A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. True False https://www.ncbi.nlm.nih.gov/data_specs/schema/other/bioproject/ [[B2AI_ORG:74]](Organization.markdown) doi:10.1093/nar/gkr1163 +[B2AI_STANDARD:228](DataStandardOrTool.markdown) BiomedicalStandard BioProject Schema NCBI BioProject XML Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:1]](DataTopic.markdown) This is a XML Schema specification of BioProject data. A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. True False https://www.ncbi.nlm.nih.gov/data_specs/schema/other/bioproject/ [[B2AI_ORG:74]](Organization.markdown) doi:10.1093/nar/gkr1163 [B2AI_STANDARD:229](DataStandardOrTool.markdown) BiomedicalStandard NCPDP F&B NCPDP Formulary and Benefit Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 Allows pharmacy benefit payers to communicate formulary and benefit Information to prescriber systems. False True https://standards.ncpdp.org/Access-to-Standards.aspx [[B2AI_ORG:63]](Organization.markdown) [B2AI_STANDARD:230](DataStandardOrTool.markdown) BiomedicalStandard NESTcc DQF NESTcc Data Quality Framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] Guiding principles and a foundation for the capture and use of high-quality data for post-market evaluation of medical devices True True https://nestcc.org/data-quality-and-methods/ https://mdic.org/wp-content/uploads/2020/02/NESTcc-Data-Quality-Framework.pdf [[B2AI_ORG:64]](Organization.markdown) [B2AI_STANDARD:231](DataStandardOrTool.markdown) BiomedicalStandard NWB Neurodata Without Borders Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 A data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build analysis tools for neurophysiology data. True False https://www.nwb.org/ https://github.com/NeurodataWithoutBorders doi:10.1101/523035 -[B2AI_STANDARD:232](DataStandardOrTool.markdown) BiomedicalStandard NIDM Neuroimaging Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:22]](DataTopic.markdown) The Neuroimaging Data Model (NIDM) is a collection of specification documents and examples that outline a domain specific extension to the W3C Provenance Data Model (PROV-DM) for the exchange and sharing of human brain imaging data. The goal of the data model is to capture data, information about the data and processes that generated the data (i.e. provenance). This information can be converted to RDF and therefore queried using SPARQL. This representation allows machine accessible representations of brain imaging data and will provide links to related resources such as publications, virtual machines, people and funding agencies. True False http://nidm.nidash.org/ [[B2AI_ORG:99]](Organization.markdown) +[B2AI_STANDARD:232](DataStandardOrTool.markdown) BiomedicalStandard NIDM Neuroimaging Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:22]](DataTopic.markdown) The Neuroimaging Data Model (NIDM) is a collection of specification documents and examples that outline a domain specific extension to the W3C Provenance Data Model (PROV-DM) for the exchange and sharing of human brain imaging data. The goal of the data model is to capture data, information about the data and processes that generated the data (i.e. provenance). This information can be converted to RDF and therefore queried using SPARQL. This representation allows machine accessible representations of brain imaging data and will provide links to related resources such as publications, virtual machines, people and funding agencies. True False http://nidm.nidash.org/ [[B2AI_ORG:99]](Organization.markdown) [B2AI_STANDARD:233](DataStandardOrTool.markdown) BiomedicalStandard NIFTI Neuroimaging Informatics Technology Initiative file format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:22]](DataTopic.markdown) The Neuroimaging Informatics Technology Initiative (nifti) file format was envisioned about a decade ago as a replacement to the then widespread, yet problematic, analyze 7.5 file format. The main problem with the previous format was perhaps the lack of adequate information about orientation in space, such that the stored data could not be unambiguously interpreted. Although the file was used by many different imaging software, the lack of adequate information on orientation obliged some, most notably spm, to include, for every analyze file, an accompanying file describing the orientation, such as a file with extension .mat. True False https://nifti.nimh.nih.gov/ https://nifti.nimh.nih.gov/nifti-2 [B2AI_STANDARD:234](DataStandardOrTool.markdown) BiomedicalStandard NeuroML NeuroML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] NeuroML is a model description language developed in XML (extensible Markup Language) that was created to facilitate data archiving, data and model exchange, database creation, and model publication in the neurosciences. One of the goals of the NeuroML project is to develop standards for model specification that will allow for greater simulator interoperability and model exchange. True False https://neuroml.org/ [B2AI_STANDARD:235](DataStandardOrTool.markdown) BiomedicalStandard NDF Neurophysiology Data Translation Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] The purpose of the Neurophysiology Data Translation Format (NDF) is to provide a means of sharing neurophysiology experimental data and derived data between services and tools developed within the CARMEN project (www.carmen.org.uk). This document specifes the NDF. The specification supports the types of data that are currently used by members of the CARMEN consortium and provides a capability to support future data types. It is capable of accommodating external data file formats as well as metadata such as user defined experimental descriptions and the history (provenance) of derived data. True False [[B2AI_ORG:11]](Organization.markdown) doi:10.3389/conf.fnins.2010.13.00118 @@ -241,20 +241,20 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:240](DataStandardOrTool.markdown) BiomedicalStandard NMR-STAR NMR Self-defining Text Archive and Retrieval format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] Format and ontology used to represent experiments, spectral and derived data, and supporting metadata. True False https://bmrb.io/standards/ [[B2AI_ORG:9]](Organization.markdown) doi:10.1007/s10858-018-0220-3 [B2AI_STANDARD:241](DataStandardOrTool.markdown) BiomedicalStandard nmrML nmrML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:17]](DataTopic.markdown) nmrML is an open mark-up language for NMR data. It is currently under heavy development and is not yet ready for public use. The development of this standard is coordinated by Workpackage 2 of the COSMOS - COordination Of Standards In MetabOlomicS Project. COSMOS is a global effort to enable free and open sharing of metabolomics data. Coordinated by Dr Christoph Steinbeck of the EMBL-European Bioinformatics Institute, COSMOS brings together European data providers to set and promote community standards that will make it easier to disseminate metabolomics data through life science e-infrastructures. This Coordination Action has been financed with €2 million by the European Commission's Seventh Framework Programme. The nmrML data standard will be approved by the Metabolomics Standards Initiative and was derived from an earlier nmrML that was developed by the Metabolomics Innovation Centre (TMIC). True False https://nmrml.org/ [[B2AI_ORG:21]](Organization.markdown) [B2AI_STANDARD:242](DataStandardOrTool.markdown) BiomedicalStandard Observ-Tab Observ-Tab format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:25]](DataTopic.markdown) Observ-Tab is a simple spreadsheet format to represent and exchange phenotype data. True False doi:10.1002/humu.22070 -[B2AI_STANDARD:243](DataStandardOrTool.markdown) BiomedicalStandard OMOP CDM Observational Medical Outcomes Partnership Common Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:4]](DataTopic.markdown) Open community data standard designed to standardize the structure and content of observational data and to enable efficient analyses that can produce reliable evidence. True False https://ohdsi.github.io/CommonDataModel/ https://github.com/OHDSI/CommonDataModel [[B2AI_ORG:76]](Organization.markdown) doi:10.3233/978-1-61499-564-7-574 -[B2AI_STANDARD:244](DataStandardOrTool.markdown) BiomedicalStandard OMOP CEM Observational Medical Outcomes Partnership Common Evidence Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:4]](DataTopic.markdown) An improved replacement to the previously reported LAERTES system. One of the initial uses of CEM has been its use in generating lists of negative control concepts to be used in empirical calibration. True False https://github.com/OHDSI/CommonEvidenceModel/wiki/Postprocessing-Negative-Controls https://github.com/OHDSI/CommonEvidenceModel [[B2AI_ORG:76]](Organization.markdown) doi:10.1007/s40264-014-0189-0 +[B2AI_STANDARD:243](DataStandardOrTool.markdown) BiomedicalStandard OMOP CDM Observational Medical Outcomes Partnership Common Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:4]](DataTopic.markdown) Open community data standard designed to standardize the structure and content of observational data and to enable efficient analyses that can produce reliable evidence. True False https://ohdsi.github.io/CommonDataModel/ https://github.com/OHDSI/CommonDataModel [[B2AI_ORG:76]](Organization.markdown) doi:10.3233/978-1-61499-564-7-574 +[B2AI_STANDARD:244](DataStandardOrTool.markdown) BiomedicalStandard OMOP CEM Observational Medical Outcomes Partnership Common Evidence Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:4]](DataTopic.markdown) An improved replacement to the previously reported LAERTES system. One of the initial uses of CEM has been its use in generating lists of negative control concepts to be used in empirical calibration. True False https://github.com/OHDSI/CommonEvidenceModel/wiki/Postprocessing-Negative-Controls https://github.com/OHDSI/CommonEvidenceModel [[B2AI_ORG:76]](Organization.markdown) doi:10.1007/s40264-014-0189-0 [B2AI_STANDARD:245](DataStandardOrTool.markdown) BiomedicalStandard OBO Open Biomedical Ontology Flat File Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:5]](DataTopic.markdown) A biology-oriented language for building ontologies, based on OWL. True False https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html https://owlcollab.github.io/oboformat/doc/obo-syntax.html [B2AI_STANDARD:246](DataStandardOrTool.markdown) BiomedicalStandard Open mHealth Open mHealth Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:18]](DataTopic.markdown) Data standards and tools for standardizing, storing, and visualizing mobile health data, including integration with FHIR standards. True False https://www.openmhealth.org/ https://github.com/openmhealth [B2AI_STANDARD:247](DataStandardOrTool.markdown) BiomedicalStandard OME-TIFF Open Microscopy Environment TIFF specification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:19]](DataTopic.markdown) multi-spectral imaging data True False https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/# [[B2AI_ORG:77]](Organization.markdown) [B2AI_STANDARD:248](DataStandardOrTool.markdown) BiomedicalStandard OME-XML Open Microscopy Environment XML format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:19]](DataTopic.markdown) OME-XML is a file format for storing microscopy information (both pixels and metadata) using the OME Data Model. True False https://docs.openmicroscopy.org/ome-model/5.6.3/ome-xml/ [[B2AI_ORG:77]](Organization.markdown) doi:10.1186/gb-2005-6-5-r47 [B2AI_STANDARD:249](DataStandardOrTool.markdown) BiomedicalStandard OMEX Open Modeling EXchange format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:27]](DataTopic.markdown) A compressed file that contains all the information needed to describe a modeling and simulation experiment. True False http://co.mbine.org/specifications/omex.version-1.pdf [[B2AI_ORG:19]](Organization.markdown) [B2AI_STANDARD:250](DataStandardOrTool.markdown) BiomedicalStandard OpenICE Open-Source Integrated Clinical Environment Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4]](DataTopic.markdown) OpenICE is an initiative to create a community implementation of an Integrated Clinical Environment. The initiative encompasses not only software implementation but also an architecture for a wider clinical ecosystem to enable new avenues of clinical research. OpenICE seeks to integrate an inclusive framework of healthcare devices and clinical applications to existing Healthcare IT ecosystems. True False https://www.openice.info/ https://github.com/mdpnp/mdpnp [[B2AI_ORG:54]](Organization.markdown) -[B2AI_STANDARD:251](DataStandardOrTool.markdown) BiomedicalStandard AOM14 openEHR Archetype Object Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:9]](DataTopic.markdown) This document contains the definitive statement of archetype semantics, in the form of an object model for archetypes. The model presented here can be used as a basis for building software that processes archetypes, independent of their persistent representation; equally, it can be used to develop the output side of parsers that process archetypes in a linguistic format, such as the openEHR Archetype Definition Language (ADL), XML-instance and so on. As a specification, it can be treated as an API for archetypes. True False https://specifications.openehr.org/releases/AM/latest/AOM1.4.html [[B2AI_ORG:79]](Organization.markdown) +[B2AI_STANDARD:251](DataStandardOrTool.markdown) BiomedicalStandard AOM14 openEHR Archetype Object Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:9]](DataTopic.markdown) This document contains the definitive statement of archetype semantics, in the form of an object model for archetypes. The model presented here can be used as a basis for building software that processes archetypes, independent of their persistent representation; equally, it can be used to develop the output side of parsers that process archetypes in a linguistic format, such as the openEHR Archetype Definition Language (ADL), XML-instance and so on. As a specification, it can be treated as an API for archetypes. True False https://specifications.openehr.org/releases/AM/latest/AOM1.4.html [[B2AI_ORG:79]](Organization.markdown) [B2AI_STANDARD:252](DataStandardOrTool.markdown) BiomedicalStandard openEHR openEHR Architecture Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:9]](DataTopic.markdown) openEHR' is the name of a technology for e-health, consisting of open specifications, clinical models and software that can be used to create standards, and build information and interoperability solutions for healthcare. The various artefacts of openEHR are produced by the openEHR community and managed by openEHR International, an international non-profit organisation originally established in 2003 and previously managed by the openEHR Foundation. True False https://www.openehr.org/about/what_is_openehr https://specifications.openehr.org/releases/BASE/latest/architecture_overview.html [[B2AI_ORG:79]](Organization.markdown) [B2AI_STANDARD:253](DataStandardOrTool.markdown) BiomedicalStandard ORION Outbreak Reports and Intervention Studies Of Nosocomial infection Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] The quality of research in hospital epidemiology (infection control) must be improved to be robust enough to influence policy and practice. In order to raise the standards of research and publication, a CONSORT equivalent for these largely quasi-experimental studies has been prepared by the authors of two relevant systematic reviews undertaken for the HTA and the Cochrane Collaboration. The statement was revised following widespread consultation with learned societies, editors of journals and researchers. It consists of a 22 item checklist, and a summary table. The emphasis is on transparency to improve the quality of reporting and on the use of appropriate statistical techniques.The statement has been endorsed and welcomed by a number of professional special interest groups and societies including the Association of Medical Microbiologists (AMM), Bristish Society for Antimicrobial Chemotherapy (BSAC) and the Infection Control Nurses' Association (ICNA) Research and Development Group. Like CONSORT, ORION considers itself a work in progress, which requires ongoing dialogue for successful promotion and dissemination. The statement is therefore offered for further public discussion and journals are encouraged to trial it as part of their reviewing and editing process and feedback to the authors. True False https://www.ucl.ac.uk/antimicrobial-resistance/reporting-guidelines/orion-statement-consort-equivalent-infection-control-intervention-studies https://www.ucl.ac.uk/drupal/site_antimicrobial-resistance/sites/antimicrobial-resistance/files/checklist_authors.pdf doi:10.1016/S1473-3099(07)70082-8 [B2AI_STANDARD:254](DataStandardOrTool.markdown) BiomedicalStandard ICE Patient-Centric Integrated Clinical Environment Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4]](DataTopic.markdown) This standard specifies the characteristics necessary for the safe integration of MEDICAL DEVICES and other equipment, via an electronic interface, from different MANUFACTURERS into a single medical system for the care of a single high acuity PATIENT. This standard establishes requirements for a medical system that is intended to have greater error resistance and improved PATIENT safety, treatment efficacy and workflow efficiency than can be achieved with independently used MEDICAL DEVICES. False False https://mdpnp.org/mdice.html https://www.astm.org/f2761-09r13.html [[B2AI_ORG:54]](Organization.markdown) [B2AI_STANDARD:255](DataStandardOrTool.markdown) BiomedicalStandard HMMER Format Pfam / HMMER Profile file format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:26]](DataTopic.markdown) The profile HMM calculated from multiple sequnce alignment data in this service is stored in Profile HMM save format (usually with .hmm extension). It is an ASCII file containing a lot of header and descriptive records followed by large numerical matrix which holds probabilistic model of the motif. The file of this format is useful to search against sequnce databases to find out other proteins which share the same motif. This HMM file should not be edited manually (especially the matrix part) because it contains consistent numerical model as a whole. True False http://hmmer.org/ https://www.genome.jp/tools/motif/hmmformat.htm -[B2AI_STANDARD:256](DataStandardOrTool.markdown) BiomedicalStandard Phenopackets Phenopackets schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:4]](DataTopic.markdown) Patient phenotypes. True False http://phenopackets.org/ https://github.com/phenopackets/phenopacket-schema [[B2AI_ORG:34|B2AI_ORG:58]](Organization.markdown) +[B2AI_STANDARD:256](DataStandardOrTool.markdown) BiomedicalStandard Phenopackets Phenopackets schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:4]](DataTopic.markdown) Patient phenotypes. True False http://phenopackets.org/ https://github.com/phenopackets/phenopacket-schema [[B2AI_ORG:34|B2AI_ORG:58]](Organization.markdown) [B2AI_STANDARD:257](DataStandardOrTool.markdown) BiomedicalStandard PHIN Guide PHIN Messaging Guide for Syndromic Surveillance Emergency Department, Urgent Care, Inpatient and Ambulatory Care Settings Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 An HL7 messaging and content reference standard for national, syndromic surveillance electronic health record technology certification; A basis for local and state syndromic surveillance messaging implementation guides; A resource for planning for the increasing use of electronic health record technology and for providing details on health data elements that may become a part of future public health syndromic surveillance messaging requirements; Optional elements of interest for adding laboratory results to syndromic surveillance messages using ORU^R01 message structure (see details in the PHIN messaging Standard, National Condition Reporting case Notification, ORU^R01 message Structure Specification profile, Version 2.1, 2014) True False https://knowledgerepository.syndromicsurveillance.org/hl7-version-251-phin-messaging-guide-syndromic-surveillance-emergency-department-urgent-care-and https://www.cdc.gov/nssp/documents/guides/syndrsurvmessagguide2_messagingguide_phn.pdf [[B2AI_ORG:40]](Organization.markdown) [B2AI_STANDARD:258](DataStandardOrTool.markdown) BiomedicalStandard phyloXML phyloXML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:5|B2AI_TOPIC:12]](DataTopic.markdown) phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch lengths, support values, and gene duplication and speciation events. True False http://www.phyloxml.org/ doi:10.1186/1471-2105-10-356 [B2AI_STANDARD:259](DataStandardOrTool.markdown) BiomedicalStandard ANSI/CTA-2056 Physical Activity Monitoring for Fitness Wearables Step Counting Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:18]](DataTopic.markdown) Definitions and performance criteria for measuring step counting on consumer wearable or app-based physical activity monitoring devices. True True https://webstore.ansi.org/standards/ansi/cta20562016ansi [[B2AI_ORG:4]](Organization.markdown) @@ -270,13 +270,13 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:269](DataStandardOrTool.markdown) BiomedicalStandard REFLECT Reporting guidelines for randomized controlled trials for livestock and food safety Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] REFLECT stands for Reporting guidElines For randomized controLled trials for livEstoCk and food safeTy. It is an evidence-based minimum set of items for trials reporting production, health, and food-safety outcomes.The aim of the REFLECT Statement is to help authors improve the reporting livestock trials with production, health, and food-safety outcomes. We have focused on both types of randomized trials, field trials and challenge studies in livestock, and the interventions may be therapeutic or preventive. The REFLECT Statement consists of a 22-item checklist (MS Word version ; PDF word version). It is an evolving document that is subject to change periodically as new evidence emerges. This website contains the current definitive version of the REFLECT Statement. True False https://meridian.cvm.iastate.edu/reflect/ doi:10.4315/0362-028x-73.3.579 [B2AI_STANDARD:270](DataStandardOrTool.markdown) BiomedicalStandard REMARK Reporting recommendations for tumour Marker prognostic studies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] Despite years of research and hundreds of reports on tumor markers in oncology, the number of markers that have emerged as clinically useful is pitifully small. Often initially reported studies of a marker show great promise, but subsequent studies on the same or related markers yield inconsistent conclusions or stand in direct contradiction to the promising results. It is imperative that we attempt to understand the reasons why multiple studies of the same marker lead to differing conclusions. A variety of methodological problems have been cited to explain these discrepancies. Unfortunately, many tumor marker studies have not been reported in a rigorous fashion, and published articles often lack sufficient information to allow adequate assessment of the quality of the study or the generalizability of study results. The development of guidelines for the reporting of tumor marker studies was a major recommendation of the National Cancer Institute-European Organisation for Research and Treatment of Cancer (NCI-EORTC) First International Meeting on Cancer Diagnostics in 2000. As for the successful CONSORT initiative for randomized trials and for the STARD statement for diagnostic studies, we suggest guidelines to provide relevant information about the study design, preplanned hypotheses, patient and specimen characteristics, assay methods, and statistical analysis methods. In addition, the guidelines provide helpful suggestions on how to present data and important elements to include in discussions. The goal of these guidelines is to encourage transparent and complete reporting so that the relevant information will be available to others to help them to judge the usefulness of the data and understand the context in which the conclusions apply. True False https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumour-marker-prognostic-studies-remark/ https://www.equator-network.org/wp-content/uploads/2016/10/REMARK-checklist-for-EQUATOR-website-002.docx doi:10.1038/sj.bjc.6602678 [B2AI_STANDARD:271](DataStandardOrTool.markdown) BiomedicalStandard ReproSchema ReproSchema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:31]](DataTopic.markdown) A common schema that encodes how the different elements of assessment data and / or the metadata relate to one another. True False https://www.repronim.org/reproschema/ https://github.com/ReproNim/reproschema -[B2AI_STANDARD:272](DataStandardOrTool.markdown) BiomedicalStandard SCDM Sentinel Common Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:9]](DataTopic.markdown) A standard data structure that allows Sentinel Data Partners to quickly execute distributed programs against local data. True False https://www.sentinelinitiative.org/methods-data-tools/sentinel-common-data-model https://dev.sentinelsystem.org/projects/SCDM/repos/sentinel_common_data_model/browse [[B2AI_ORG:89]](Organization.markdown) +[B2AI_STANDARD:272](DataStandardOrTool.markdown) BiomedicalStandard SCDM Sentinel Common Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:9]](DataTopic.markdown) A standard data structure that allows Sentinel Data Partners to quickly execute distributed programs against local data. True False https://www.sentinelinitiative.org/methods-data-tools/sentinel-common-data-model https://dev.sentinelsystem.org/projects/SCDM/repos/sentinel_common_data_model/browse [[B2AI_ORG:89]](Organization.markdown) [B2AI_STANDARD:273](DataStandardOrTool.markdown) BiomedicalStandard SAM Sequence Alignment/Map Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] The Sequence Alignment/Map (SAM) format is a TAB-delimited text format consisting of a header section, which is optional, and an alignment section. True False http://samtools.sourceforge.net/ doi:10.1093/bioinformatics/btp352 -[B2AI_STANDARD:274](DataStandardOrTool.markdown) BiomedicalStandard SRA-XML Sequence Read Archive Metadata XML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:12|B2AI_TOPIC:13|B2AI_TOPIC:33]](DataTopic.markdown) Used by The Sequence Read Archive (SRA) and the European Nucleotide Archive (ENA) to store raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. True False https://www.ncbi.nlm.nih.gov/sra/docs/submitmeta/ [[B2AI_ORG:74]](Organization.markdown) doi:10.1093/nar/gkq1019 +[B2AI_STANDARD:274](DataStandardOrTool.markdown) BiomedicalStandard SRA-XML Sequence Read Archive Metadata XML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:12|B2AI_TOPIC:13|B2AI_TOPIC:33]](DataTopic.markdown) Used by The Sequence Read Archive (SRA) and the European Nucleotide Archive (ENA) to store raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. True False https://www.ncbi.nlm.nih.gov/sra/docs/submitmeta/ [[B2AI_ORG:74]](Organization.markdown) doi:10.1093/nar/gkq1019 [B2AI_STANDARD:275](DataStandardOrTool.markdown) BiomedicalStandard SOFT Simple Omnibus Format in Text Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:5]](DataTopic.markdown) Simple Omnibus Format in Text (SOFT) is designed for rapid batch submission (and download) of data. SOFT is a simple line-based, plain text format, meaning that SOFT files may be readily generated from common spreadsheet and database applications. A single SOFT file can hold both data tables and accompanying descriptive information for multiple, concatenated Platforms, Samples, and/or Series records. True False https://www.ncbi.nlm.nih.gov/geo/info/soft-seq.html [B2AI_STANDARD:276](DataStandardOrTool.markdown) BiomedicalStandard SMILES Simplified Molecular Input Line Entry Specification Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:3]](DataTopic.markdown) A typographical line notation for specifying chemical structure. True False http://opensmiles.org/ http://opensmiles.org/opensmiles.html [B2AI_STANDARD:277](DataStandardOrTool.markdown) BiomedicalStandard SED-ML Simulation Experiment Description Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:5]](DataTopic.markdown) SED-ML is an XML-based format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments. It follows the requirements defined in the MIASE guidelines. True False https://sed-ml.org/ -[B2AI_STANDARD:278](DataStandardOrTool.markdown) BiomedicalStandard SPDI SPDI data model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:12|B2AI_TOPIC:13|B2AI_TOPIC:35]](DataTopic.markdown) Sequence variant data model. Represents all variants as a sequence of four operations. Start at the boundary before the first nucleotide in the sequence S, advance P nucleotides, delete D nucleotides, then Insert the nucleotides in the string. True False [[B2AI_ORG:74]](Organization.markdown) doi:10.1093/bioinformatics/btz856 +[B2AI_STANDARD:278](DataStandardOrTool.markdown) BiomedicalStandard SPDI SPDI data model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:12|B2AI_TOPIC:13|B2AI_TOPIC:35]](DataTopic.markdown) Sequence variant data model. Represents all variants as a sequence of four operations. Start at the boundary before the first nucleotide in the sequence S, advance P nucleotides, delete D nucleotides, then Insert the nucleotides in the string. True False [[B2AI_ORG:74]](Organization.markdown) doi:10.1093/bioinformatics/btz856 [B2AI_STANDARD:279](DataStandardOrTool.markdown) BiomedicalStandard SEDS Standard EEG Data Structure Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:37]](DataTopic.markdown) A new and more flexible data structure, named the Standard EEG Data Structure (SEDS), was proposed to meet the needs of both small-scale EEG data batch processing in single-site studies and large-scale EEG data sharing and analysis in single-/multisite studies (especially on cloud platforms). False False doi:10.1016/j.softx.2021.100933 [B2AI_STANDARD:280](DataStandardOrTool.markdown) BiomedicalStandard SPREC Standard PREanalytical Code Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [codesystem] [[B2AI_TOPIC:9]](DataTopic.markdown) The ISBER Biospecimen Science Working Group has developed a SPREC that identifies and records the main pre-analytical factors that may have impact on the integrity of sampled clinical fluids and solid biospecimens and their simple derivatives during collection, processing and storage. SPREC comprises 7 elements for both fluid and solid samples, defining the sample and primary container type, periods of cold and warm ischemia, and subsequent handling steps including speed and temperature of centrifugation and final storage temperature. The ability to manage and track pre-analytical variations impacting biospecimen integrity is fundamental to the provision of high quality tissue samples for research, and the effective and efficient interconnectivity and interoperability between national and international Biobanks. True False https://www.isber.org/page/SPREC [[B2AI_ORG:48]](Organization.markdown) doi:10.1089/bio.2017.0109 [B2AI_STANDARD:281](DataStandardOrTool.markdown) BiomedicalStandard STARD Standards for Reporting of Diagnostic Accuracy Studies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] The objective of the STARD initiative is to improve the accuracy and completeness of reporting of studies of diagnostic accuracy, to allow readers to assess the potential for bias in the study (internal validity) and to evaluate its generalisability (external validity).The STARD statement consist of a checklist of 25 items and recommends the use of a flow diagram which describe the design of the study and the flow of patients. True False https://www.equator-network.org/reporting-guidelines/stard/ doi:10.1136/bmjopen-2016-012799 @@ -290,7 +290,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:289](DataStandardOrTool.markdown) BiomedicalStandard SBML Systems Biology Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:1]](DataTopic.markdown) The Systems Biology Markup Language (SBML) is a machine-readable exchange format for computational models of biological processes. Its strength is in representating phenomena at the scale of biochemical reactions, but it is not limited to that. By supporting SBML as an input and output format, different software tools can operate on the same representation of a model, removing chances for errors in translation and assuring a common starting point for analyses and simulations. True False http://sbml.org/ [[B2AI_ORG:19]](Organization.markdown) doi:10.1515/jib-2017-0081 [B2AI_STANDARD:290](DataStandardOrTool.markdown) BiomedicalStandard SBRML Systems Biology Results Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:1]](DataTopic.markdown) Systems Biology has benefited tremendously from the development and use of SBML, which is a markup language to specify models composed of molecular species, and their interactions (including reactions). SBML is a common format that many systems biology software understand and thus it has become the way in which models are shared and communicated. Despite the popularity of SBML, that has resulted in many models being available in electronic format, there is currently no standard way of communicating the results of the operations carried out with such models (e.g. simulations). Here we propose a new markup language which is complementary to SBML and which is intended to specify results from operations carried out on models SBRML. In fact, this markup language is useful also to communicate experimental data as long as it is possible to express the data in terms of a reference SBML model. Thus SBRML is a means of specifying quantitative results in the context of a systems biology model. False False https://sbrml.sourceforge.net/SBRML/Welcome.html [B2AI_STANDARD:291](DataStandardOrTool.markdown) BiomedicalStandard Tabix Tabix index file format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:13]](DataTopic.markdown) A tab-delimited genome position index file format. The format can handle individual chromosomes up to 512 Mbp (2^29 bases) in length. True False http://www.htslib.org/doc/tabix.html https://samtools.github.io/hts-specs/tabix.pdf doi:10.1093/bioinformatics/btq671 -[B2AI_STANDARD:292](DataStandardOrTool.markdown) BiomedicalStandard TCS Taxonomic Concept Transfer Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] The development of an abstract model for a taxonomic concept, which can capture the various models represented and understood by the various data providers, is central to this project. This model is presented as an XML schema document that is proposed as a standard to allow exchange of data between different data models. It aims to capture data as understood by the data owners without distortion, and facilitate the query of different data resources according to the common schema model. The TCS schema was conceived to allow the representation of taxonomic concepts as defined in published taxonomic classifications, revisions and databases. As such, it specifies the structure for XML documents to be used for the transfer of defined concepts. Valid transfer documents may either explicitly detail the defining components of taxon concepts, transfer GUIDs referring to defined taxon concepts (if and when these are available) or a mixture of the two. True False http://www.tdwg.org/standards/117 https://github.com/tdwg/tcs [[B2AI_ORG:93]](Organization.markdown) +[B2AI_STANDARD:292](DataStandardOrTool.markdown) BiomedicalStandard TCS Taxonomic Concept Transfer Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] The development of an abstract model for a taxonomic concept, which can capture the various models represented and understood by the various data providers, is central to this project. This model is presented as an XML schema document that is proposed as a standard to allow exchange of data between different data models. It aims to capture data as understood by the data owners without distortion, and facilitate the query of different data resources according to the common schema model. The TCS schema was conceived to allow the representation of taxonomic concepts as defined in published taxonomic classifications, revisions and databases. As such, it specifies the structure for XML documents to be used for the transfer of defined concepts. Valid transfer documents may either explicitly detail the defining components of taxon concepts, transfer GUIDs referring to defined taxon concepts (if and when these are available) or a mixture of the two. True False http://www.tdwg.org/standards/117 https://github.com/tdwg/tcs [[B2AI_ORG:93]](Organization.markdown) [B2AI_STANDARD:293](DataStandardOrTool.markdown) BiomedicalStandard TDWG SDS Taxonomic Databases Working Group Standards Documentation Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 This document defines how TDWG standards should be presented. Each standard is a logical directory or folder containing two or more files - a cover page outlining basic meta data for the standard and one or more normative files specifying the standard itself. Rules are specified for the naming of standards and files. Human readable files should be in English, follow basic layout principles and be marked up in XHTML. The legal statements that all documents must contain are defined. True False http://www.tdwg.org/standards/147 [[B2AI_ORG:93]](Organization.markdown) [B2AI_STANDARD:294](DataStandardOrTool.markdown) BiomedicalStandard ToxML ToxML standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:3]](DataTopic.markdown) ToxML is an open data exchange standard that allows the representation and communication of toxicological and related data in a well-structured electronic format. True False doi:10.1080/1062936X.2013.783506 [B2AI_STANDARD:295](DataStandardOrTool.markdown) BiomedicalStandard TREND Transparent Reporting of Evaluations with Nonrandomized Designs Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [guidelines] Evidence-based public health decisions are based on evaluations of intervention studies with randomized and nonrandomized designs. Transparent reporting is crucial for assessing the validity and efficacy of these intervention studies, and, it facilitates synthesis of the findings for evidence-based recommendations. Therefore, the mission of the Transparent Reporting of Evaluations with Nonrandomized Designs (TREND) group is to improve the reporting standards of nonrandomized evaluations of behavioral and public health intervention True False https://www.cdc.gov/trendstatement/index.html https://www.cdc.gov/trendstatement/pdf/trendstatement_TREND_Checklist.pdf [[B2AI_ORG:12]](Organization.markdown) doi:10.2105/ajph.94.3.361 @@ -352,10 +352,10 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:351](DataStandardOrTool.markdown) DataStandard MP3 MPEG-1 Audio Layer 3 \\| MPEG-2 Audio Layer 3 Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [audiovisual|fileformat] [[B2AI_TOPIC:37]](DataTopic.markdown) MP3 (formally MPEG-1 Audio Layer III or MPEG-2 Audio Layer III) is a coding format for digital audio. True False https://en.wikipedia.org/wiki/MP3 https://www.iso.org/standard/26797.html [B2AI_STANDARD:352](DataStandardOrTool.markdown) DataStandard MPEG-4 MPEG-4 Part 14 digital multimedia container format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [audiovisual|fileformat] [[B2AI_TOPIC:15|B2AI_TOPIC:37]](DataTopic.markdown) A digital multimedia container format most commonly used to store video and audio, but it can also be used to store other data such as subtitles and still images. Like most modern container formats, it allows streaming over the Internet. True False https://en.wikipedia.org/wiki/MP4_file_format https://www.loc.gov/preservation/digital/formats/fdd/fdd000155.shtml [[B2AI_ORG:49]](Organization.markdown) [B2AI_STANDARD:353](DataStandardOrTool.markdown) DataStandard netCDF Network Common Data Form Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] A standardized format for chromatographic data representation. True False https://www.unidata.ucar.edu/software/netcdf/ https://www.astm.org/e1947-98r14.html [[B2AI_ORG:8]](Organization.markdown) -[B2AI_STANDARD:354](DataStandardOrTool.markdown) DataStandard NNEF Neural Network Exchange Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:5]](DataTopic.markdown) An exchange format for neural network models produced using Torch, Caffe, TensorFlow, Theano, Chainer, Caffe2, PyTorch, or MXNet. True False https://www.khronos.org/nnef https://github.com/KhronosGroup/NNEF-Tools +[B2AI_STANDARD:354](DataStandardOrTool.markdown) DataStandard NNEF Neural Network Exchange Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) An exchange format for neural network models produced using Torch, Caffe, TensorFlow, Theano, Chainer, Caffe2, PyTorch, or MXNet. True False https://www.khronos.org/nnef https://github.com/KhronosGroup/NNEF-Tools [B2AI_STANDARD:355](DataStandardOrTool.markdown) DataStandard OMXML OGC and ISO Observations and Measurements standard in XML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [markuplanguage] [[B2AI_TOPIC:5]](DataTopic.markdown) This standard specifies an XML implementation for the OGC and ISO Observations and Measurements (O&M) conceptual model (OGC Observations and Measurements v2.0 also published as ISO/DIS 19156), including a schema for Sampling Features. This encoding is an essential dependency for the OGC Sensor Observation Service (SOS) Interface Standard. More specifically, this standard defines XML schemas for observations, and for features involved in sampling when making observations. These provide document models for the exchange of information describing observation acts and their results, both within and between different scientific and technical communities. True False https://www.ogc.org/standards/om [[B2AI_ORG:49]](Organization.markdown) [B2AI_STANDARD:356](DataStandardOrTool.markdown) DataStandard OGG Speex Ogg Speex Audio Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [audiovisual|fileformat] [[B2AI_TOPIC:37]](DataTopic.markdown) File format and bitstream encoding for for spoken content, targeted at a wide range of devices other than mobile phones. True False https://speex.org/docs/manual/speex-manual/node8.html -[B2AI_STANDARD:357](DataStandardOrTool.markdown) DataStandard ONNX Open Neural Network Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:5]](DataTopic.markdown) ONNX is an open format built to represent machine learning models. True False https://onnx.ai/ https://github.com/onnx/onnx/blob/main/docs/IR.md +[B2AI_STANDARD:357](DataStandardOrTool.markdown) DataStandard ONNX Open Neural Network Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) ONNX is an open format built to represent machine learning models. True False https://onnx.ai/ https://github.com/onnx/onnx/blob/main/docs/IR.md [B2AI_STANDARD:358](DataStandardOrTool.markdown) DataStandard OpenAPI OpenAPI Specification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Standard for describing program interfaces. True False https://spec.openapis.org/oas/latest.html https://github.com/OAI/OpenAPI-Specification/ [B2AI_STANDARD:359](DataStandardOrTool.markdown) DataStandard parquet Parquet Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [fileformat] [[B2AI_TOPIC:5]](DataTopic.markdown) Apache Parquet is a free and open-source column-oriented data storage format in the Apache Hadoop ecosystem. True False https://parquet.apache.org/ [B2AI_STANDARD:360](DataStandardOrTool.markdown) DataStandard PURL Persistent Uniform Resource Locator Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) PURLs are Web addresses or Uniform Resource Locators (URLs) that act as permanent identifiers in the face of a dynamic and changing Web infrastructure. Instead of resolving directly to Web resources (documents, data, services, people, etc.) PURLs provide a level of indirection that allows the underlying Web addresses of resources to change over time without negatively affecting systems that depend on them. This capability provides continuity of references to network resources that may migrate from machine to machine for business, social or technical reasons. True False https://sites.google.com/site/persistenturls/ https://code.google.com/archive/p/persistenturls/ [[B2AI_ORG:43]](Organization.markdown) @@ -405,7 +405,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:404](DataStandardOrTool.markdown) OntologyOrVocabulary ADO Alzheimer's Disease Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [obofoundry] [[B2AI_TOPIC:7]](DataTopic.markdown) concepts related to Alzheimer's Disease True False https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO [B2AI_STANDARD:405](DataStandardOrTool.markdown) OntologyOrVocabulary ARO Antibiotic Resistance Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [obofoundry] Antibiotic resistance genes and mutations True False https://github.com/arpcard/aro doi:10.1093/nar/gkz935 [B2AI_STANDARD:406](DataStandardOrTool.markdown) OntologyOrVocabulary APOLLO_SV Apollo Structured Vocabulary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [obofoundry] Terms and relations for interoperation between epidemic models and public health application software. True False https://github.com/ApolloDev/apollo-sv -[B2AI_STANDARD:407](DataStandardOrTool.markdown) OntologyOrVocabulary AIO Artificial Intelligence Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) General terms for AI True False https://bioportal.bioontology.org/ontologies/AIO https://github.com/berkeleybop/artificial-intelligence-ontology +[B2AI_STANDARD:407](DataStandardOrTool.markdown) OntologyOrVocabulary AIO Artificial Intelligence Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) General terms for AI True False https://bioportal.bioontology.org/ontologies/AIO https://github.com/berkeleybop/artificial-intelligence-ontology [B2AI_STANDARD:408](DataStandardOrTool.markdown) OntologyOrVocabulary BFO Basic Formal Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [obofoundry] [[B2AI_TOPIC:5]](DataTopic.markdown) Upper level ontology. True False http://basic-formal-ontology.org/ https://github.com/BFO-ontology/BFO doi:10.3233/AO-160164 [B2AI_STANDARD:409](DataStandardOrTool.markdown) OntologyOrVocabulary BCO Biological Collections Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [obofoundry] Biodiversity data, including data on museum collections and environmental/metagenomic samples. True False https://github.com/BiodiversityOntologies/bco [B2AI_STANDARD:410](DataStandardOrTool.markdown) OntologyOrVocabulary FBBI Biological Imaging Methods Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [obofoundry] [[B2AI_TOPIC:15]](DataTopic.markdown) Sample preparation, visualization and imaging methods used in biomedical research. True False http://cellimagelibrary.org/ https://github.com/CRBS/Biological_Imaging_Methods_Ontology/ @@ -473,7 +473,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:472](DataStandardOrTool.markdown) OntologyOrVocabulary IAO Information Artifact Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [obofoundry] [[B2AI_TOPIC:5]](DataTopic.markdown) An ontology of information entities. True False https://github.com/information-artifact-ontology/IAO [B2AI_STANDARD:473](DataStandardOrTool.markdown) OntologyOrVocabulary ICO Informed Consent Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [obofoundry] [[B2AI_TOPIC:4]](DataTopic.markdown) An ontology of clinical informed consents True False https://github.com/ICO-ontology/ICO [B2AI_STANDARD:474](DataStandardOrTool.markdown) OntologyOrVocabulary ICEO Integrative and Conjugative Element Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [obofoundry] An integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs). True False http://db-mml.sjtu.edu.cn/ICEberg/ https://github.com/ontoice/ICEO doi:10.1038/s41597-021-01112-5 -[B2AI_STANDARD:475](DataStandardOrTool.markdown) OntologyOrVocabulary ITO Intelligence Task Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Comprehensive, curated and interlinked data of artificial intelligence tasks, benchmarks, AI performance metrics, benchmark results and research papers. True False https://openbiolink.github.io/ITOExplorer/ https://github.com/OpenBioLink/ITO [[B2AI_ORG:87]](Organization.markdown) +[B2AI_STANDARD:475](DataStandardOrTool.markdown) OntologyOrVocabulary ITO Intelligence Task Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) Comprehensive, curated and interlinked data of artificial intelligence tasks, benchmarks, AI performance metrics, benchmark results and research papers. True False https://openbiolink.github.io/ITOExplorer/ https://github.com/OpenBioLink/ITO [[B2AI_ORG:87]](Organization.markdown) [B2AI_STANDARD:476](DataStandardOrTool.markdown) OntologyOrVocabulary INO Interaction Network Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [obofoundry] An ontology of interactions and interaction networks. True False https://github.com/INO-ontology/ino doi:10.1186/2041-1480-6-2 [B2AI_STANDARD:477](DataStandardOrTool.markdown) OntologyOrVocabulary IOBC Interlinking Ontology for Biological Concepts Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:1]](DataTopic.markdown) biological, biomedical, and related concepts True False https://github.com/kushidat/IOBC doi:10.1007/s00354-019-00074-y [B2AI_STANDARD:478](DataStandardOrTool.markdown) OntologyOrVocabulary KISAO Kinetic Simulation Algorithm Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [obofoundry] Algorithms for simulating biology, their parameters, and their outputs. True False http://co.mbine.org/standards/kisao https://github.com/SED-ML/KiSAO @@ -685,11 +685,11 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:684](DataStandardOrTool.markdown) ReferenceDataOrDataset VoxPopuli VoxPopuli Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [speechdata] [[B2AI_TOPIC:36]](DataTopic.markdown) 100K hours of unlabelled speech data for 23 languages, 1.8K hours of transcribed speech data for 16 languages, and 17.3K hours of speech-to-speech interpretation data for 16x15 directions. True False https://github.com/facebookresearch/voxpopuli doi:10.18653/v1/2021.acl-long.80 [B2AI_STANDARD:685](DataStandardOrTool.markdown) ReferenceDataOrDataset WHODrug WHODrug medicinal information dictionary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [drugdata] [[B2AI_TOPIC:8]](DataTopic.markdown) WHODrug contains individual trade names, active ingredients and additional information such as marketing authorisation holder, country of sale, pharmaceutical form and strength. All related medications are linked using a structured WHODrug alphanumeric code, connecting trade names and variation of the ingredient with the active moiety of the ingredient. True True https://who-umc.org/whodrug/whodrug-global/ https://who-umc.org/whodrug/whodrug-global/applications/download-area/ doi:10.1007/s43441-020-00130-6 [B2AI_STANDARD:686](DataStandardOrTool.markdown) ReferenceDataOrDataset WikiPathways WikiPathways database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:21]](DataTopic.markdown) WikiPathways is a database of biological pathways maintained by and for the scientific community. True False https://www.wikipathways.org/index.php/WikiPathways doi:10.1093/nar/gkaa1024 -[B2AI_STANDARD:687](DataStandardOrTool.markdown) ReferenceImplementation Gupta2021 A DICOM Standard Pipeline for Microscope Imaging Modalities Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:19]](DataTopic.markdown) This paper proposed a pipeline for the integration of multiple microscopy imaging modalities into the PACS-DICOM universe, including the numerous metadata elements. A proof-of-concept system was developed, for validation purposes, and integrated with the Dicoogle open-source PACS, providing image storage, metadata indexing and visualization. False True [[B2AI_ORG:25]](Organization.markdown) doi:10.1109/ISCC53001.2021.9631529 +[B2AI_STANDARD:687](DataStandardOrTool.markdown) ReferenceImplementation Gupta2021 A DICOM Standard Pipeline for Microscope Imaging Modalities Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:19]](DataTopic.markdown) This paper proposed a pipeline for the integration of multiple microscopy imaging modalities into the PACS-DICOM universe, including the numerous metadata elements. A proof-of-concept system was developed, for validation purposes, and integrated with the Dicoogle open-source PACS, providing image storage, metadata indexing and visualization. False True [[B2AI_ORG:25]](Organization.markdown) doi:10.1109/ISCC53001.2021.9631529 [B2AI_STANDARD:688](DataStandardOrTool.markdown) ReferenceImplementation MukhiyaLamo2021 An HL7 FHIR and GraphQL approach for interoperability between heterogeneous Electronic Health Record systems Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:9]](DataTopic.markdown) ...we offer an architecture that utilizes a resource server based on GraphQL and HL7 FHIR that establishes communication between two heterogeneous EHRs. This paper describes how the proposed architecture is implemented to achieve interoperability between two heterogeneous EHRs, HL7 FHIR and OpenMRS. The presented approach establishes secure communication between the EHRs and provides accurate mappings that enable timely health information exchange between EHRs. True False [[B2AI_ORG:40]](Organization.markdown) doi:10.1177/14604582211043920 [B2AI_STANDARD:689](DataStandardOrTool.markdown) ReferenceImplementation Tapuria2018 Comparison and transformation between CDISC ODM and EN13606 EHR standards in connecting EHR data with clinical trial research data Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4|B2AI_TOPIC:9]](DataTopic.markdown) This work investigates the mapping and data interoperability between healthcare and research standards - EN13606 used for the EHRs and the Clinical Data Interchange Standards Consortium Operational Data Model (CDISC ODM) used for clinical research. True False [[B2AI_ORG:15|B2AI_ORG:79]](Organization.markdown) doi:10.1177/2055207618777676 [B2AI_STANDARD:690](DataStandardOrTool.markdown) ReferenceImplementation Biderman2022 Datasheet for the Pile Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datasheets] [[B2AI_TOPIC:32]](DataTopic.markdown) This datasheet describes the Pile, a 825 GiB dataset of human-authored text compiled by EleutherAI for use in large-scale language modeling. The Pile is comprised of 22 different text sources, ranging from original scrapes done for this project, to text data made available by the data owners, to third-party scrapes available online. True False doi:0.48550/arXiv.2201.07311 -[B2AI_STANDARD:691](DataStandardOrTool.markdown) ReferenceImplementation Kalen2021 Design and Implementation of the Pre-Clinical DICOM Standard in Multi-Cohort Murine Studies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) The small animal imaging Digital Imaging and Communications in Medicine (DICOM) acquisition context structured report (SR) was developed to incorporate pre-clinical data in an established DICOM format for rapid queries and comparison of clinical and non-clinical datasets. Established terminologies (i.e., anesthesia, mouse model nomenclature, veterinary definitions, NCI Metathesaurus) were utilized to assist in defining terms implemented in pre-clinical imaging and new codes were added to integrate the specific small animal procedures and handling processes, such as housing, biosafety level, and pre-imaging rodent preparation. True False [[B2AI_ORG:25]](Organization.markdown) doi:10.3390/tomography7010001 +[B2AI_STANDARD:691](DataStandardOrTool.markdown) ReferenceImplementation Kalen2021 Design and Implementation of the Pre-Clinical DICOM Standard in Multi-Cohort Murine Studies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] [[B2AI_TOPIC:15]](DataTopic.markdown) The small animal imaging Digital Imaging and Communications in Medicine (DICOM) acquisition context structured report (SR) was developed to incorporate pre-clinical data in an established DICOM format for rapid queries and comparison of clinical and non-clinical datasets. Established terminologies (i.e., anesthesia, mouse model nomenclature, veterinary definitions, NCI Metathesaurus) were utilized to assist in defining terms implemented in pre-clinical imaging and new codes were added to integrate the specific small animal procedures and handling processes, such as housing, biosafety level, and pre-imaging rodent preparation. True False [[B2AI_ORG:25]](Organization.markdown) doi:10.3390/tomography7010001 [B2AI_STANDARD:692](DataStandardOrTool.markdown) ReferenceImplementation Xiao2022 FHIR-Ontop-OMOP - Building clinical knowledge graphs in FHIR RDF with the OMOP Common data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [multimodal] We developed a system called FHIR-Ontop-OMOP to generate virtual clinical KGs from the OMOP relational databases. We leveraged an OMOP CDM-based Medical Information Mart for Intensive Care (MIMIC-III) data repository to evaluate the FHIR-Ontop-OMOP system in terms of the faithfulness of data transformation and the conformance of the generated CKGs to the FHIR RDF specification. True False https://github.com/fhircat/FHIROntopOMOP [[B2AI_ORG:40|B2AI_ORG:76]](Organization.markdown) doi:10.1016/j.jbi.2022.104201 [B2AI_STANDARD:693](DataStandardOrTool.markdown) ReferenceImplementation Murugan2021 Genomic considerations for FHIR; eMERGE implementation lessons Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:9|B2AI_TOPIC:13]](DataTopic.markdown) The Electronic Medical Records and Genomics (eMERGE) Network’s Phase III program initially used a commercially developed XML message format for standardized and structured representation of genetic results for electronic health record (EHR) integration. In a desire to move towards a standard representation, the network created a new standardized format based upon Health Level Seven Fast Healthcare Interoperability Resources (HL7® FHIR®), to represent clinical genomics results. These new standards improve the utility of HL7® FHIR® as an international healthcare interoperability standard for management of genetic data from patients. True False [[B2AI_ORG:40]](Organization.markdown) doi:10.1016/j.jbi.2021.103795 [B2AI_STANDARD:694](DataStandardOrTool.markdown) ReferenceImplementation HAPI FHIR HAPI FHIR Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4]](DataTopic.markdown) A complete implementation of the HL7 FHIR standard for healthcare interoperability in Java. True False https://hapifhir.io/ @@ -700,13 +700,13 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:699](DataStandardOrTool.markdown) ReferenceImplementation Pasini2022 matRadiomics - A Novel and Complete Radiomics Framework, from Image Visualization to Predictive Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4|B2AI_TOPIC:15]](DataTopic.markdown) Using a single tool, i) biomedical images can be imported and inspected, ii) the target can be identified and segmented, iii) features can be extracted from the target, iv) reduced and selected, and v) used to build a predictive model using machine learning algorithms. As result, two different feature extractors can be chosen, a Matlab-based extractor, and the Pyradiomics extractor naturally integrated into matRadiomics. True False [[B2AI_ORG:25]](Organization.markdown) doi:10.3390/jimaging8080221 [B2AI_STANDARD:700](DataStandardOrTool.markdown) ReferenceImplementation PatientTM Modelling patient trajectories using multimodal information Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [multimodal] We propose a solution to model patient trajectories that combines different types of information (e.g. clinical text, standard codes) and considers the temporal aspect of clinical data. This solution leverages two different architectures - one supporting flexible sets of input features, to convert patient admissions into dense representations; and a second exploring extracted admission representations in a recurrent-based architecture, where patient trajectories are processed in sub-sequences using a sliding window mechanism. True False https://github.com/bioinformatics-ua/PatientTM doi:10.1016/j.jbi.2022.104195 [B2AI_STANDARD:701](DataStandardOrTool.markdown) ReferenceImplementation Garbin2021 Structured dataset documentation - a datasheet for CheXpert Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datasheets] [[B2AI_TOPIC:15]](DataTopic.markdown) Following the structured format of Datasheets for Datasets, this paper expands on the original CheXpert paper and other sources to show the critical role played by radiologists in the creation of reliable labels and to describe the different aspects of the dataset composition in detail. Such structured documentation intends to increase the awareness in the machine learning and medical communities of the strengths, applications, and evolution of CheXpert, thereby advancing the field of medical image analysis. True False doi:10.48550/arXiv.2105.03020 -[B2AI_STANDARD:702](DataStandardOrTool.markdown) ReferenceImplementation Kvak2022 Towards Clinical Practice - Design and Implementation of Convolutional Neural Network-Based Assistive Diagnosis System for COVID-19 Case Detection from Chest X-Ray Images Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 One of the critical tools for early detection and subsequent evaluation of the incidence of lung diseases is chest radiography. This study presents a real-world implementation of a convolutional neural network (CNN) based Carebot Covid app to detect COVID-19 from chest X-ray (CXR) images. Our proposed model takes the form of a simple and intuitive application. Used CNN can be deployed as a STOW-RS prediction endpoint for direct implementation into DICOM viewers. True False [[B2AI_ORG:25]](Organization.markdown) doi:10.48550/arXiv.2203.10596 +[B2AI_STANDARD:702](DataStandardOrTool.markdown) ReferenceImplementation Kvak2022 Towards Clinical Practice - Design and Implementation of Convolutional Neural Network-Based Assistive Diagnosis System for COVID-19 Case Detection from Chest X-Ray Images Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [has_ai_application] One of the critical tools for early detection and subsequent evaluation of the incidence of lung diseases is chest radiography. This study presents a real-world implementation of a convolutional neural network (CNN) based Carebot Covid app to detect COVID-19 from chest X-ray (CXR) images. Our proposed model takes the form of a simple and intuitive application. Used CNN can be deployed as a STOW-RS prediction endpoint for direct implementation into DICOM viewers. True False [[B2AI_ORG:25]](Organization.markdown) doi:10.48550/arXiv.2203.10596 [B2AI_STANDARD:703](DataStandardOrTool.markdown) ReferenceImplementation Papez2022 Transforming and evaluating the UK Biobank to the OMOP Common Data Model for COVID-19 research and beyond Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 We converted UK Biobank data to OMOP CDM v. 5.3. We transformed participant research data on diseases collected at recruitment and electronic health records (EHR) from primary care, hospitalizations, cancer registrations, and mortality from providers in England, Scotland, and Wales. We performed syntactic and semantic validations and compared comorbidities and risk factors between source and transformed data. True False [[B2AI_ORG:76]](Organization.markdown) doi:10.1093/jamia/ocac203 [B2AI_STANDARD:704](DataStandardOrTool.markdown) Registry bio.tools bio.tools Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [dataregistry|softwareregistry] [[B2AI_TOPIC:1]](DataTopic.markdown) Registry of software tools, databases and services for bioinformatics and the life sciences. True False https://bio.tools/ https://github.com/bio-tools/biotoolsregistry/ [B2AI_STANDARD:705](DataStandardOrTool.markdown) Registry Bioconductor Bioconductor Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [softwareregistry] [[B2AI_TOPIC:5]](DataTopic.markdown) The mission of the Bioconductor project is to develop, support, and disseminate free open source software that facilitates rigorous and reproducible analysis of data from current and emerging biological assays. We are dedicated to building a diverse, collaborative, and welcoming community of developers and data scientists. True False https://www.bioconductor.org/ https://github.com/Bioconductor/BiocManager [B2AI_STANDARD:706](DataStandardOrTool.markdown) Registry BioPortal BioPortal Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [ontologyregistry] [[B2AI_TOPIC:1]](DataTopic.markdown) An ontology registry. True False https://bioportal.bioontology.org/ https://github.com/ncbo [B2AI_STANDARD:707](DataStandardOrTool.markdown) Registry Bioregistry Bioregistry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [standardsregistry] [[B2AI_TOPIC:5]](DataTopic.markdown) A registry of prefixes and identifier formats used in biomedical data sets, knowledge bases, and ontologies. True False https://bioregistry.io/ https://github.com/biopragmatics/bioregistry doi:10.1101/2022.07.08.499378 -[B2AI_STANDARD:708](DataStandardOrTool.markdown) Registry Bridge2AI registry Bridge to Artificial Intelligence Registry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [standardsregistry] [[B2AI_TOPIC:5]](DataTopic.markdown) Standards, tools, reference implementations, and related resources. True False https://github.com/bridge2ai/b2ai-standards-registry +[B2AI_STANDARD:708](DataStandardOrTool.markdown) Registry Bridge2AI registry Bridge to Artificial Intelligence Registry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [standardsregistry|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) Standards, tools, reference implementations, and related resources. True False https://github.com/bridge2ai/b2ai-standards-registry [B2AI_STANDARD:709](DataStandardOrTool.markdown) Registry CDISC SHARE CDISC Shared Health And Research Electronic library Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 CDISC launched the CDISC Shared Health And Research Electronic library (SHARE) to provide the standards metadata in machine-readable formats to facilitate the automated management and implementation of the standards. True True https://www.cdisc.org/faq/share/what-cdisc-share [[B2AI_ORG:15]](Organization.markdown) PUBMED:29888049 [B2AI_STANDARD:710](DataStandardOrTool.markdown) Registry Database Commons Database Commons Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) A catalog of worldwide biological databases maintained by the China National Center for Bioinformation, True False https://ngdc.cncb.ac.cn/databasecommons/ doi:10.1016/j.gpb.2022.12.004 [B2AI_STANDARD:711](DataStandardOrTool.markdown) Registry Dockstore Dockstore Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [softwareregistry] [[B2AI_TOPIC:5]](DataTopic.markdown) A free and open source platform for sharing reusable and scalable analytical tools and workflows. True False https://dockstore.org/ https://github.com/dockstore/dockstore [[B2AI_ORG:34]](Organization.markdown) @@ -720,7 +720,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:719](DataStandardOrTool.markdown) Registry 3DP Registry RSNA-ACR 3D Printing Registry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [dataregistry] The joint RSNA and American College of Radiology (ACR) 3D printing clinical data registry collects 3D printing data at the point of clinical care. With the goal of improving both patient care and characterizing resource utilization, the brand-new registry collects anonymized 3D printing case information, clinical indications and intended uses for printed models, source imaging, model construction techniques and effort, 3D printing techniques and effort, and the clinical impact of the models. False True https://www.rsna.org/practice-tools/RSNA-ACR-3D-printing-registry [[B2AI_ORG:85]](Organization.markdown) [B2AI_STANDARD:720](DataStandardOrTool.markdown) SoftwareOrTool clinical-problem-standardization A corpus-driven standardization framework for encoding clinical problems with HL7 FHIR Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4]](DataTopic.markdown) A framework for transforming free-text problem descriptions into standardized Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) models. True False https://github.com/OHNLP/clinical-problem-standardization [[B2AI_ORG:40]](Organization.markdown) doi:10.1016/j.jbi.2020.103541 [B2AI_STANDARD:721](DataStandardOrTool.markdown) SoftwareOrTool ARES A Research Exploration System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4]](DataTopic.markdown) A Research Exploration System designed to improved the transparency of observational data research. ARES is an opinionated framework that delineates three levels of observational data assessment. True False https://github.com/OHDSI/Ares [[B2AI_ORG:76]](Organization.markdown) -[B2AI_STANDARD:722](DataStandardOrTool.markdown) SoftwareOrTool Aesara Aesara Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework] [[B2AI_TOPIC:5]](DataTopic.markdown) Aesara is a Python library that allows one to define, optimize, and efficiently evaluate mathematical expressions involving multi-dimensional arrays. True False https://github.com/aesara-devs/aesara +[B2AI_STANDARD:722](DataStandardOrTool.markdown) SoftwareOrTool Aesara Aesara Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) Aesara is a Python library that allows one to define, optimize, and efficiently evaluate mathematical expressions involving multi-dimensional arrays. True False https://github.com/aesara-devs/aesara [B2AI_STANDARD:723](DataStandardOrTool.markdown) SoftwareOrTool AWS Amazon Web Services Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [cloudservice] [[B2AI_TOPIC:5]](DataTopic.markdown) Cloud computing platform. False True https://aws.amazon.com/ [B2AI_STANDARD:724](DataStandardOrTool.markdown) SoftwareOrTool Amundsen Amundsen Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Amundsen is a data discovery and metadata engine for improving the productivity of data analysts, data scientists and engineers when interacting with data. It does that today by indexing data resources (tables, dashboards, streams, etc.) and powering a page-rank style search based on usage patterns (e.g. highly queried tables show up earlier than less queried tables). True False https://www.amundsen.io/ https://github.com/amundsen-io/amundsen [B2AI_STANDARD:725](DataStandardOrTool.markdown) SoftwareOrTool Anduril Anduril Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [toolkit] [[B2AI_TOPIC:20]](DataTopic.markdown) Anduril is a workflow platform for analyzing large data sets. Anduril provides facilities for analyzing high-thoughput data in biomedical research, and the platform is fully extensible by third parties. True False https://anduril.org/site/ https://bitbucket.org/anduril-dev/anduril/src/stable/ doi:10.1093/bioinformatics/btz133 @@ -743,7 +743,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:742](DataStandardOrTool.markdown) SoftwareOrTool Comet Comet Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Platform for managing machine learning models. False True https://www.comet.com/ https://github.com/comet-ml [B2AI_STANDARD:743](DataStandardOrTool.markdown) SoftwareOrTool CDAPS Community Detection APplication and Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:12|B2AI_TOPIC:21]](DataTopic.markdown) Performs multiscale community detection and functional enrichment for network analysis through a service-oriented architecture. These features are provided by integrating popular community detection algorithms and enrichment tools. All the algorithms and tools run remotely on a dedicated server. True False https://cdaps.readthedocs.io/ https://github.com/cytoscape/cy-community-detection doi:10.1371/journal.pcbi.1008239 [B2AI_STANDARD:744](DataStandardOrTool.markdown) SoftwareOrTool CD-CLiXO Community Detection CliXO Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:12|B2AI_TOPIC:21]](DataTopic.markdown) Builds a CDAPS compatible community detection Docker image using CliXO. True False https://github.com/idekerlab/cdclixo -[B2AI_STANDARD:745](DataStandardOrTool.markdown) SoftwareOrTool CORAL Contextual Ontology-based Repository Analysis Library Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:5]](DataTopic.markdown) A framework for rigorous self-validated data modeling and integrative, reproducible data analysis True False https://github.com/jmchandonia/CORAL doi:10.1093/gigascience/giac089 +[B2AI_STANDARD:745](DataStandardOrTool.markdown) SoftwareOrTool CORAL Contextual Ontology-based Repository Analysis Library Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) A framework for rigorous self-validated data modeling and integrative, reproducible data analysis True False https://github.com/jmchandonia/CORAL doi:10.1093/gigascience/giac089 [B2AI_STANDARD:746](DataStandardOrTool.markdown) SoftwareOrTool CML library Continuous Machine Learning Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Continuous Machine Learning (CML) is an open-source library for implementing continuous integration & delivery (CI/CD) in machine learning projects. Use it to automate parts of your development workflow, including model training and evaluation, comparing ML experiments across your project history, and monitoring changing datasets. True False https://cml.dev/ https://github.com/iterative/cml [B2AI_STANDARD:747](DataStandardOrTool.markdown) SoftwareOrTool Cromwell Cromwell Workflow Management System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Cromwell is an open-source Workflow Management System for bioinformatics. True False https://cromwell.readthedocs.io/en/stable/ https://github.com/broadinstitute/cromwell doi:10.7490/f1000research.1114634.1 [B2AI_STANDARD:748](DataStandardOrTool.markdown) SoftwareOrTool Cytoscape Cytoscape software Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:21]](DataTopic.markdown) An open source software platform for visualizing complex networks and integrating these with any type of attribute data. True False https://cytoscape.org/ https://github.com/cytoscape/cytoscape @@ -754,7 +754,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:753](DataStandardOrTool.markdown) SoftwareOrTool DataHub DataHub Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) An open-source metadata platform. True False https://datahubproject.io/ https://github.com/linkedin/datahub [B2AI_STANDARD:754](DataStandardOrTool.markdown) SoftwareOrTool Datasette Datasette Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) A tool for exploring and publishing data. It helps people take data of any shape, analyze and explore it, and publish it as an interactive website and accompanying API. True False https://datasette.io/ https://github.com/simonw/datasette [B2AI_STANDARD:755](DataStandardOrTool.markdown) SoftwareOrTool DENDRO DENDRO Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [scrnaseqanalysis] [[B2AI_TOPIC:34]](DataTopic.markdown) An analysis method for scRNA-seq data that clusters single cells into genetically distinct subclones and reconstructs the phylogenetic tree relating the subclones. True False https://github.com/zhouzilu/DENDRO doi:10.1186/s13059-019-1922-x -[B2AI_STANDARD:756](DataStandardOrTool.markdown) SoftwareOrTool Determined Determined Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework] [[B2AI_TOPIC:5]](DataTopic.markdown) Determined is an open-source deep learning training platform. True False https://www.determined.ai/ https://github.com/determined-ai/determined +[B2AI_STANDARD:756](DataStandardOrTool.markdown) SoftwareOrTool Determined Determined Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) Determined is an open-source deep learning training platform. True False https://www.determined.ai/ https://github.com/determined-ai/determined [B2AI_STANDARD:757](DataStandardOrTool.markdown) SoftwareOrTool Dicoogle Dicoogle Picture Archiving and Communications System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) Dicoogle is an open source Picture Archiving and Communications System (PACS) archive. Its modular architecture allows the quick development of new functionalities, due the availability of a Software Development Kit (SDK). True False https://dicoogle.com/ https://github.com/bioinformatics-ua/dicoogle doi:10.1109/ISCC50000.2020.9219545 [B2AI_STANDARD:758](DataStandardOrTool.markdown) SoftwareOrTool DigitalOcean DigitalOcean Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [cloudservice] [[B2AI_TOPIC:5]](DataTopic.markdown) Cloud computing platform. False True https://www.digitalocean.com/ [B2AI_STANDARD:759](DataStandardOrTool.markdown) SoftwareOrTool DoubletDecon DoubletDecon Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [scrnaseqanalysis] [[B2AI_TOPIC:34]](DataTopic.markdown) An approach that detects doublet cell capture artifacts in scRNA-seq data with a combination of deconvolution analyses and the identification of unique cell-state gene expression. True False https://github.com/EDePasquale/DoubletDecon doi:10.1016/j.celrep.2019.09.082 @@ -763,14 +763,14 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:762](DataStandardOrTool.markdown) SoftwareOrTool ENHANCE Expression denoising heuristic using aggregation of neighbors and principal component extraction Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [scrnaseqanalysis] [[B2AI_TOPIC:34]](DataTopic.markdown) A simple denoising strategy for scRNA-seq data based on principal component analysis (PCA). True False https://github.com/yanailab/enhance doi:10.1101/655365 [B2AI_STANDARD:763](DataStandardOrTool.markdown) SoftwareOrTool FDP FAIR Data Point Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) FAIR Data Point (FDP) is a REST API for creating, storing, and serving FAIR metadata. This FDP implementation also presents a Web-based graphical user interface (GUI). The metadata contents are generated semi-automatically according to the FAIR Data Point software specification document. True False https://github.com/FAIRDataTeam/FAIRDataPoint doi:10.1162/dint_a_00160 [B2AI_STANDARD:764](DataStandardOrTool.markdown) SoftwareOrTool FAIRSCAPE FAIRSCAPE digital commons framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) A reusable computational framework, enabling simplified access to modern scalable cloud-based components. FAIRSCAPE fully implements the FAIR data principles and extends them to provide fully FAIR Evidence, including machine-interpretable provenance of datasets, software and computations, as metadata for all computed results. True False https://fairscape.github.io/ https://github.com/fairscape/fairscape doi:10.1007/s12021-021-09529-4 -[B2AI_STANDARD:765](DataStandardOrTool.markdown) SoftwareOrTool FastAI FastAI Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework] [[B2AI_TOPIC:5]](DataTopic.markdown) fastai is a deep learning library which provides practitioners with high-level components that can quickly and easily provide state-of-the-art results in standard deep learning domains, and provides researchers with low-level components that can be mixed and matched to build new approaches. It aims to do both things without substantial compromises in ease of use, flexibility, or performance. This is possible thanks to a carefully layered architecture, which expresses common underlying patterns of many deep learning and data processing techniques in terms of decoupled abstractions. These abstractions can be expressed concisely and clearly by leveraging the dynamism of the underlying Python language and the flexibility of the PyTorch library. True False https://github.com/fastai/fastai +[B2AI_STANDARD:765](DataStandardOrTool.markdown) SoftwareOrTool FastAI FastAI Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) fastai is a deep learning library which provides practitioners with high-level components that can quickly and easily provide state-of-the-art results in standard deep learning domains, and provides researchers with low-level components that can be mixed and matched to build new approaches. It aims to do both things without substantial compromises in ease of use, flexibility, or performance. This is possible thanks to a carefully layered architecture, which expresses common underlying patterns of many deep learning and data processing techniques in terms of decoupled abstractions. These abstractions can be expressed concisely and clearly by leveraging the dynamism of the underlying Python language and the flexibility of the PyTorch library. True False https://github.com/fastai/fastai [B2AI_STANDARD:766](DataStandardOrTool.markdown) SoftwareOrTool Galaxy Galaxy Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [toolkit] [[B2AI_TOPIC:20]](DataTopic.markdown) Galaxy is an open source, web-based platform for data intensive biomedical research. True False https://usegalaxy.org/ https://github.com/galaxyproject/galaxy doi:10.1093/nar/gky379 [B2AI_STANDARD:767](DataStandardOrTool.markdown) SoftwareOrTool GCP Google Cloud Platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [cloudservice] [[B2AI_TOPIC:5]](DataTopic.markdown) Cloud computing platform. False True https://cloud.google.com/ [[B2AI_ORG:37]](Organization.markdown) -[B2AI_STANDARD:768](DataStandardOrTool.markdown) SoftwareOrTool GrAPE Graph Representation leArning, Predictions and Evaluation library Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [graphdataplatform|machinelearningframework] [[B2AI_TOPIC:21]](DataTopic.markdown) A fast graph processing and embedding library, designed to scale with big graphs and to run on both off-the-shelf laptop and desktop computers and High Performance Computing clusters of workstations. True False https://github.com/AnacletoLAB/grape doi:10.48550/arXiv.2110.06196 +[B2AI_STANDARD:768](DataStandardOrTool.markdown) SoftwareOrTool GrAPE Graph Representation leArning, Predictions and Evaluation library Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [graphdataplatform|machinelearningframework|has_ai_application] [[B2AI_TOPIC:21]](DataTopic.markdown) A fast graph processing and embedding library, designed to scale with big graphs and to run on both off-the-shelf laptop and desktop computers and High Performance Computing clusters of workstations. True False https://github.com/AnacletoLAB/grape doi:10.48550/arXiv.2110.06196 [B2AI_STANDARD:769](DataStandardOrTool.markdown) SoftwareOrTool HESML Half-Edge Semantic Measures Library Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:32|B2AI_TOPIC:16]](DataTopic.markdown) HESML is an efficient, scalable and large Java software library of ontology-based semantic similarity measures and Information Content (IC) models based on WordNet, SNOMED-CT, MeSH or any other OBO-based ontology. True False http://hesml.lsi.uned.es/ https://github.com/jjlastra/HESML doi:10.1186/S12859-021-04539-0 [B2AI_STANDARD:770](DataStandardOrTool.markdown) SoftwareOrTool Hangar Hangar Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Version control for tensor data. True False https://hangar-py.readthedocs.io/en/stable/ https://github.com/tensorwerk/hangar-py [B2AI_STANDARD:771](DataStandardOrTool.markdown) SoftwareOrTool HADES Health Analytics Data-to-Evidence Suite Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4]](DataTopic.markdown) HADES (formally known as the OHDSI Methods Library) is a set of open source R packages for large scale analytics, including population characterization, population-level causal effect estimation, and patient-level prediction. True False https://ohdsi.github.io/Hades/ https://github.com/OHDSI/Hades [[B2AI_ORG:76]](Organization.markdown) -[B2AI_STANDARD:772](DataStandardOrTool.markdown) SoftwareOrTool HAIM Holistic AI in Medicine framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [multimodal] A unified Holistic AI in Medicine (HAIM) framework to facilitate the generation and testing of AI systems that leverage multimodal inputs. True False https://github.com/lrsoenksen/HAIM doi:10.1038/s41746-022-00689-4 +[B2AI_STANDARD:772](DataStandardOrTool.markdown) SoftwareOrTool HAIM Holistic AI in Medicine framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [multimodal|has_ai_application] A unified Holistic AI in Medicine (HAIM) framework to facilitate the generation and testing of AI systems that leverage multimodal inputs. True False https://github.com/lrsoenksen/HAIM doi:10.1038/s41746-022-00689-4 [B2AI_STANDARD:773](DataStandardOrTool.markdown) SoftwareOrTool HTSeq HTSeq Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:13]](DataTopic.markdown) A Python library to facilitate the rapid development of high throughput sequencing data analysis scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. True False https://github.com/htseq/htseq doi:10.1093/bioinformatics/btu638 [B2AI_STANDARD:774](DataStandardOrTool.markdown) SoftwareOrTool ImJoy ImJoy Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:15]](DataTopic.markdown) A plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. ImJoy runs on mobile and desktop environment cross different operating systems, plugins can run in the browser, localhost, remote and cloud servers. True False https://imjoy.io/ https://github.com/imjoy-team/ImJoy doi:10.1038/s41592-019-0627-0 [B2AI_STANDARD:775](DataStandardOrTool.markdown) SoftwareOrTool i2b2 Informatics for Integrating Biology and the Bedside platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:9]](DataTopic.markdown) A system for searching and exchanging clinical data. True False https://www.i2b2.org/software/index.html https://github.com/i2b2 [[B2AI_ORG:42]](Organization.markdown) doi:10.1093/jamia/ocv188 @@ -786,13 +786,13 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:785](DataStandardOrTool.markdown) SoftwareOrTool Linode Linode Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [cloudservice] [[B2AI_TOPIC:5]](DataTopic.markdown) Cloud computing platform. False True https://www.linode.com/ [B2AI_STANDARD:786](DataStandardOrTool.markdown) SoftwareOrTool MAGIC Markov Affinity-based Graph Imputation of Cells Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [scrnaseqanalysis] [[B2AI_TOPIC:34]](DataTopic.markdown) A method for imputing missing values in scRNA-seq data. True False https://www.krishnaswamylab.org/projects/magic https://github.com/KrishnaswamyLab/MAGIC doi:10.1016/j.cell.2018.05.061 [B2AI_STANDARD:787](DataStandardOrTool.markdown) SoftwareOrTool Marquez Marquez Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Marquez is an open source metadata service for the collection, aggregation, and visualization of a data ecosystem's metadata. It maintains the provenance of how datasets are consumed and produced, provides global visibility into job runtime and frequency of dataset access, centralization of dataset lifecycle management, and much more. Marquez was released and open sourced by WeWork. True False https://lfaidata.foundation/projects/marquez/ https://github.com/MarquezProject/marquez -[B2AI_STANDARD:788](DataStandardOrTool.markdown) SoftwareOrTool MONAI Medical Open Network for AI Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework] [[B2AI_TOPIC:5]](DataTopic.markdown) MONAI is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem. True False https://monai.io/ https://github.com/Project-MONAI/MONAI +[B2AI_STANDARD:788](DataStandardOrTool.markdown) SoftwareOrTool MONAI Medical Open Network for AI Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) MONAI is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem. True False https://monai.io/ https://github.com/Project-MONAI/MONAI [B2AI_STANDARD:789](DataStandardOrTool.markdown) SoftwareOrTool Metacat Metacat Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Metacat is a unified metadata exploration API service. You can explore Hive, RDS, Teradata, Redshift, S3 and Cassandra. Metacat provides you information about what data you have, where it resides and how to process it. True False https://github.com/Netflix/metacat [[B2AI_ORG:65]](Organization.markdown) [B2AI_STANDARD:790](DataStandardOrTool.markdown) SoftwareOrTool Azure Microsoft Azure Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [cloudservice] [[B2AI_TOPIC:5]](DataTopic.markdown) Cloud computing platform. False True https://azure.microsoft.com/ [[B2AI_ORG:56]](Organization.markdown) [B2AI_STANDARD:791](DataStandardOrTool.markdown) SoftwareOrTool MinIO MinIO Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [cloudservice] [[B2AI_TOPIC:5]](DataTopic.markdown) S3 compatible object storage. Native to Kubernetes, MinIO is the only object storage suite available on every public cloud, every Kubernetes distribution, the private cloud and the edge. MinIO is software-defined and is 100% open source under GNU AGPL v3. True False https://min.io/ https://github.com/minio/ [B2AI_STANDARD:792](DataStandardOrTool.markdown) SoftwareOrTool MLMD ML Metadata Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) ML Metadata (MLMD) is a library for recording and retrieving metadata associated with ML developer and data scientist workflows. True False https://www.tensorflow.org/tfx/guide/mlmd https://github.com/google/ml-metadata [[B2AI_ORG:37]](Organization.markdown) [B2AI_STANDARD:793](DataStandardOrTool.markdown) SoftwareOrTool MLflow MLflow platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) MLflow is an open source platform to manage the ML lifecycle, including experimentation, reproducibility, deployment, and a central model registry True False https://mlflow.org/ https://github.com/mlflow/mlflow/ -[B2AI_STANDARD:794](DataStandardOrTool.markdown) SoftwareOrTool MLPro MLPro framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework] [[B2AI_TOPIC:5]](DataTopic.markdown) Embeds flexible and recombinable ML models into standardized processes for training and real operations. In addition, it integrates numerous common open source frameworks and thus standardizes their use. True False https://mlpro.readthedocs.io/ https://github.com/fhswf/MLPro doi:10.1016/j.simpa.2022.100421 +[B2AI_STANDARD:794](DataStandardOrTool.markdown) SoftwareOrTool MLPro MLPro framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) Embeds flexible and recombinable ML models into standardized processes for training and real operations. In addition, it integrates numerous common open source frameworks and thus standardizes their use. True False https://mlpro.readthedocs.io/ https://github.com/fhswf/MLPro doi:10.1016/j.simpa.2022.100421 [B2AI_STANDARD:795](DataStandardOrTool.markdown) SoftwareOrTool MoClust MoClust Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [scrnaseqanalysis] [[B2AI_TOPIC:23]](DataTopic.markdown) A novel joint clustering framework that can be applied to several types of single-cell multi-omics data. A selective automatic doublet detection module that can identify and filter out doublets is introduced in the pretraining stage to improve data quality. Omics-specific autoencoders are introduced to characterize the multi-omics data. True False https://zenodo.org/record/7306504 doi:10.1093/bioinformatics/btac736 [B2AI_STANDARD:796](DataStandardOrTool.markdown) SoftwareOrTool MCT Model Card Toolkit Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [modelcards] [[B2AI_TOPIC:5]](DataTopic.markdown) The Model Card Toolkit (MCT) streamlines and automates generation of Model Cards, machine learning documents that provide context and transparency into a model's development and performance. True False https://github.com/tensorflow/model-card-toolkit [[B2AI_ORG:37]](Organization.markdown) doi:10.48550/arXiv.1810.03993 [B2AI_STANDARD:797](DataStandardOrTool.markdown) SoftwareOrTool MongoDB MongoDB Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) A non-relational document database that provides support for JSON-like storage. True False https://www.mongodb.com/ https://github.com/mongodb/mongo @@ -804,7 +804,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:803](DataStandardOrTool.markdown) SoftwareOrTool NETME NETME Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:16]](DataTopic.markdown) Starting from a set of fulltext obtained from PubMed, through an easy-to-use web interface, interactively extracts a group of biological elements stored into a selected list of ontological databases and then synthesizes a network with inferred relations among such elements. True False https://netme.click/#/ doi:10.1007/S41109-021-00435-X [B2AI_STANDARD:804](DataStandardOrTool.markdown) SoftwareOrTool NetSeekR NetSeekR network analysis R package Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [scrnaseqanalysis] [[B2AI_TOPIC:34]](DataTopic.markdown) A network analysis pipeline for RNA-Seq time series data. True False https://github.com/igbb-popescu-lab/NetSeekR doi:10.1186/S12859-021-04554-1 [B2AI_STANDARD:805](DataStandardOrTool.markdown) SoftwareOrTool NDEx Network Data Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [graphdataplatform] [[B2AI_TOPIC:21]](DataTopic.markdown) The NDEx Project provides an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge. True True https://www.ndexbio.org/ -[B2AI_STANDARD:806](DataStandardOrTool.markdown) SoftwareOrTool NeuCA NeuCA - Neural-network based Cell Annotation tool Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [scrnaseqanalysis] [[B2AI_TOPIC:34]](DataTopic.markdown) A R/Bioconductor tool for cell type annotation using single-cell RNA-seq data. It is a supervised cell label assignment method that uses existing scRNA-seq data with known labels to train a neural network-based classifier, and then predict cell labels in single-cell RNA-seq data of interest. True False https://github.com/haoharryfeng/NeuCA doi:10.1038/s41598-021-04473-4 +[B2AI_STANDARD:806](DataStandardOrTool.markdown) SoftwareOrTool NeuCA NeuCA - Neural-network based Cell Annotation tool Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [scrnaseqanalysis|has_ai_application] [[B2AI_TOPIC:34]](DataTopic.markdown) A R/Bioconductor tool for cell type annotation using single-cell RNA-seq data. It is a supervised cell label assignment method that uses existing scRNA-seq data with known labels to train a neural network-based classifier, and then predict cell labels in single-cell RNA-seq data of interest. True False https://github.com/haoharryfeng/NeuCA doi:10.1038/s41598-021-04473-4 [B2AI_STANDARD:807](DataStandardOrTool.markdown) SoftwareOrTool Nextflow Nextflow Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:20]](DataTopic.markdown) Enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. True False https://www.nextflow.io/ https://github.com/nextflow-io/nextflow [[B2AI_ORG:90]](Organization.markdown) [B2AI_STANDARD:808](DataStandardOrTool.markdown) SoftwareOrTool AnVIL NHGRI Analysis Visualization and Informatics Lab-space Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [cloudplatform] [[B2AI_TOPIC:13]](DataTopic.markdown) AnVIL is NHGRI's Genomic Data Science Analysis, Visualization, and Informatics Lab-Space. True True https://anvilproject.org/ https://github.com/anvilproject [[B2AI_ORG:73]](Organization.markdown) [B2AI_STANDARD:809](DataStandardOrTool.markdown) SoftwareOrTool OmicsEV OmicsEV Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:23]](DataTopic.markdown) An R package for quality evaluation of omics data tables. For each data table, OmicsEV uses a series of methods to evaluate data depth, data normalization, batch effect, biological signal, platform reproducibility, and multi-omics concordance, producing comprehensive visual and quantitative evaluation results that help assess data quality of individual data tables and facilitate the identification of the optimal data processing method and parameters for the omics study under investigation. True False https://github.com/bzhanglab/OmicsEV doi:10.1093/bioinformatics/btac698 @@ -814,11 +814,11 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:813](DataStandardOrTool.markdown) SoftwareOrTool pandas pandas Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) An open source data analysis and manipulation tool built on top of the Python programming language. True False https://pandas.pydata.org/ [B2AI_STANDARD:814](DataStandardOrTool.markdown) SoftwareOrTool Panel Panel Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datavisualization] [[B2AI_TOPIC:5]](DataTopic.markdown) An open-source Python library that lets you create custom interactive web apps and dashboards by connecting user-defined widgets to plots, images, tables, or text. True False https://panel.holoviz.org/ https://github.com/holoviz/panel [B2AI_STANDARD:815](DataStandardOrTool.markdown) SoftwareOrTool PostgreSQL PostgreSQL Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) An open source object-relational database system. True False https://www.postgresql.org/ https://github.com/postgres/postgres -[B2AI_STANDARD:816](DataStandardOrTool.markdown) SoftwareOrTool PyTorch PyTorch Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework] [[B2AI_TOPIC:5]](DataTopic.markdown) A popular machine learning platform. True False https://pytorch.org/ https://github.com/pytorch/pytorch +[B2AI_STANDARD:816](DataStandardOrTool.markdown) SoftwareOrTool PyTorch PyTorch Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) A popular machine learning platform. True False https://pytorch.org/ https://github.com/pytorch/pytorch [B2AI_STANDARD:817](DataStandardOrTool.markdown) SoftwareOrTool Quarto Quarto publishing system Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [notebookplatform] [[B2AI_TOPIC:5]](DataTopic.markdown) An open-source scientific and technical publishing system built on Pandoc. True False https://quarto.org/ https://github.com/quarto-dev/quarto-cli [B2AI_STANDARD:818](DataStandardOrTool.markdown) SoftwareOrTool RDCA-DAP Rare Disease Cures Accelerator-Data and Analytics Platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [cloudplatform] [[B2AI_TOPIC:4]](DataTopic.markdown) The Rare Disease Cures Accelerator-Data and Analytics Platform (RDCA-DAP®) is an FDA-funded initiative that provides a centralized and standardized infrastructure to support and accelerate rare disease characterization, with the goal of accelerating therapy development across rare diseases. False True https://c-path.org/programs/rdca-dap/ [[B2AI_ORG:31]](Organization.markdown) [B2AI_STANDARD:819](DataStandardOrTool.markdown) SoftwareOrTool refget refget API Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:13]](DataTopic.markdown) Enables access to reference genomic sequences without ambiguity from different databases and servers using a checksum identifier based on the sequence content itself. True False https://samtools.github.io/hts-specs/refget.html [[B2AI_ORG:34]](Organization.markdown) -[B2AI_STANDARD:820](DataStandardOrTool.markdown) SoftwareOrTool Relexi Relexi Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework] [[B2AI_TOPIC:5]](DataTopic.markdown) Relexi is an open source reinforcement learning (RL) framework written in Python and based on TensorFlow’s RL library TF-Agents. Relexi allows to employ RL for environments that require computationally intensive simulations like applications in computational fluid dynamics. For this, Relexi couples legacy simulation codes with the RL library TF-Agents at scale on modern high-performance computing (HPC) hardware using the SmartSim library. Relexi thus provides an easy way to explore the potential of RL for HPC applications. True False https://github.com/flexi-framework/relexi doi:10.1016/j.simpa.2022.100422 +[B2AI_STANDARD:820](DataStandardOrTool.markdown) SoftwareOrTool Relexi Relexi Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) Relexi is an open source reinforcement learning (RL) framework written in Python and based on TensorFlow’s RL library TF-Agents. Relexi allows to employ RL for environments that require computationally intensive simulations like applications in computational fluid dynamics. For this, Relexi couples legacy simulation codes with the RL library TF-Agents at scale on modern high-performance computing (HPC) hardware using the SmartSim library. Relexi thus provides an easy way to explore the potential of RL for HPC applications. True False https://github.com/flexi-framework/relexi doi:10.1016/j.simpa.2022.100422 [B2AI_STANDARD:821](DataStandardOrTool.markdown) SoftwareOrTool REDCap Research Electronic Data Capture Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:31]](DataTopic.markdown) Electronic data capture software and workflow methodology for designing clinical and translational research databases. True True https://www.project-redcap.org/ doi:10.1016/j.jbi.2008.08.010 [B2AI_STANDARD:822](DataStandardOrTool.markdown) SoftwareOrTool Synapse Sage Synapse Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Synapse is a set of web services and tools that make it easier for researchers to aggregate, organize, analyze, and share scientific data, code, and insights. True True https://www.synapse.org/ https://github.com/Sage-Bionetworks/Synapse-Repository-Services [[B2AI_ORG:86]](Organization.markdown) doi:10.2139/ssrn.3502410 [B2AI_STANDARD:823](DataStandardOrTool.markdown) SoftwareOrTool SemEHR SemEHR Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:9]](DataTopic.markdown) An open source semantic search and analytics tool for EHRs. True False https://github.com/CogStack/CogStack-SemEHR doi:10.1093/jamia/ocx160 @@ -829,10 +829,10 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:828](DataStandardOrTool.markdown) SoftwareOrTool STAR Spliced Transcripts Alignment to a Reference Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:33]](DataTopic.markdown) Software based on an RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. True False https://github.com/alexdobin/STAR doi:10.1093/bioinformatics/bts635 [B2AI_STANDARD:829](DataStandardOrTool.markdown) SoftwareOrTool SyBLaRS Systems Biology Layout and Rendering Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) A web service for automatic layout of biological data in various standard formats as well as construction of customized images in both raster image and scalable vector formats of these maps. Some of the supported standards are more generic such as GraphML and JSON, whereas others are specialized to biology such as SBGNML (The Systems Biology Graphical Notation Markup Language) and SBML (The Systems Biology Markup Language). True False http://syblars.cs.bilkent.edu.tr/ https://github.com/iVis-at-Bilkent/syblars doi:10.1371/journal.pcbi.1010635 [B2AI_STANDARD:830](DataStandardOrTool.markdown) SoftwareOrTool TES Task Execution Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) standardized schema and API for describing and executing batch execution tasks True False https://ga4gh.github.io/task-execution-schemas/docs/ [[B2AI_ORG:34]](Organization.markdown) -[B2AI_STANDARD:831](DataStandardOrTool.markdown) SoftwareOrTool TF Tensorflow Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework] [[B2AI_TOPIC:5]](DataTopic.markdown) A popular machine learning platform. True False https://www.tensorflow.org/ https://github.com/tensorflow/tensorflow [[B2AI_ORG:37]](Organization.markdown) +[B2AI_STANDARD:831](DataStandardOrTool.markdown) SoftwareOrTool TF Tensorflow Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) A popular machine learning platform. True False https://www.tensorflow.org/ https://github.com/tensorflow/tensorflow [[B2AI_ORG:37]](Organization.markdown) [B2AI_STANDARD:832](DataStandardOrTool.markdown) SoftwareOrTool Terra Terra Community Workbench Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [cloudplatform] [[B2AI_TOPIC:20]](DataTopic.markdown) Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate. True True https://app.terra.bio/ https://github.com/DataBiosphere/terra-ui [[B2AI_ORG:71]](Organization.markdown) [B2AI_STANDARD:833](DataStandardOrTool.markdown) SoftwareOrTool R The R Project for Statistical Computing Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) A free software environment for statistical computing and graphics. True False https://www.r-project.org/ -[B2AI_STANDARD:834](DataStandardOrTool.markdown) SoftwareOrTool Theano Theano Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [deprecated|machinelearningframework] [[B2AI_TOPIC:5]](DataTopic.markdown) A Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It is being continued as aesara. True False https://github.com/Theano/Theano +[B2AI_STANDARD:834](DataStandardOrTool.markdown) SoftwareOrTool Theano Theano Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [deprecated|machinelearningframework|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) A Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It is being continued as aesara. True False https://github.com/Theano/Theano [B2AI_STANDARD:835](DataStandardOrTool.markdown) SoftwareOrTool TRS Tool Registry Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) common API for describing tools in registries True False https://ga4gh.github.io/tool-registry-service-schemas/ [[B2AI_ORG:34]](Organization.markdown) [B2AI_STANDARD:836](DataStandardOrTool.markdown) SoftwareOrTool U-BRITE UAB Biomedical Research Information Technology Enhancement Commons Program Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:4|B2AI_TOPIC:13]](DataTopic.markdown) U-BRITE (UAB Biomedical Research Information Technology Enhancement) assembles new and existing HIPAA-compliant, high-performance informatics tools to provide researchers with a means to better manage and analyze clinical and genomic data sets and implements a “translational research commons” to facilitate and enable interdisciplinary team science across geographical locations. False True https://ubrite.org/ [[B2AI_ORG:94]](Organization.markdown) [B2AI_STANDARD:837](DataStandardOrTool.markdown) SoftwareOrTool Usagi Usagi Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) An application to help create mappings between coding systems and the Vocabulary standard concepts. True False https://github.com/OHDSI/Usagi [[B2AI_ORG:76]](Organization.markdown) @@ -841,7 +841,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:840](DataStandardOrTool.markdown) SoftwareOrTool W&B Weights and Balances platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Platform for tracking, comparing, and visualizing machine learning experiments. True True https://wandb.ai/ [B2AI_STANDARD:841](DataStandardOrTool.markdown) SoftwareOrTool WES Workflow Execution Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Standard for submitting workflow requests to workflow execution systems. True False https://ga4gh.github.io/workflow-execution-service-schemas/docs/ [[B2AI_ORG:34]](Organization.markdown) [B2AI_STANDARD:842](DataStandardOrTool.markdown) SoftwareOrTool Xethub Xethub Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) Git-based collaboration to large scale repositories of data, code, or any combination of files. True True https://xethub.com/assets/docs/ -[B2AI_STANDARD:843](DataStandardOrTool.markdown) SoftwareOrTool ZenML ZenML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework] [[B2AI_TOPIC:5]](DataTopic.markdown) ZenML is an extensible, open-source MLOps framework for creating portable, production-ready MLOps pipelines. True False https://zenml.io/ https://github.com/zenml-io/zenml +[B2AI_STANDARD:843](DataStandardOrTool.markdown) SoftwareOrTool ZenML ZenML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [machinelearningframework|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) ZenML is an extensible, open-source MLOps framework for creating portable, production-ready MLOps pipelines. True False https://zenml.io/ https://github.com/zenml-io/zenml [B2AI_STANDARD:844](DataStandardOrTool.markdown) TrainingProgram OHDSI Tutorials 2019 OHDSI Tutorials - OMOP Common Data Model and Standardized Vocabularies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 This workshop is for data holders who want to apply OHDSI’s data standards to their own observational datasets and researchers who want to be aware of OHDSI’s data standards, so they can leverage data in OMOP CDM format for their own research purposes. True False https://www.ohdsi.org/2019-tutorials-omop-common-data-model-and-standardized-vocabularies/ https://github.com/OHDSI/Tutorial-CDM [[B2AI_ORG:76]](Organization.markdown) [B2AI_STANDARD:845](DataStandardOrTool.markdown) DataStandardOrTool CDC Introduction to FHIR CDC Introduction to FHIR - Training Recordings Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 A series of HL7 FAIR training lecture recordings made available through YouTube. True False https://www.cdc.gov/nchs/data/nvss/modernization/Introductory-Training-FHIR.pdf [[B2AI_ORG:40]](Organization.markdown) [B2AI_STANDARD:846](DataStandardOrTool.markdown) TrainingProgram FHIR Drills FHIR Drills Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 This set of pages contains a series of FHIR tutorials for those just beginning to learn the new specification. The tutorials require no prior knowledge of FHIR or REST. At present these tutorials are in their beta stage of development and we would appreciate any feedback you may have as we plan to build upon these in time to create a full set of tutorials from the very basic to the more complex. True False https://fhir-drills.github.io/ [[B2AI_ORG:40]](Organization.markdown) @@ -866,7 +866,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:865](DataStandardOrTool.markdown) ReferenceDataOrDataset DANDI Distributed Archives for Neurophysiology Data Integration Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:22]](DataTopic.markdown) An archive for cellular neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, and images from immunostaining experiments. True False https://www.dandiarchive.org/ 2023-04-10 [B2AI_STANDARD:866](DataStandardOrTool.markdown) OntologyOrVocabulary SALON Sequence Alignment Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:23]](DataTopic.markdown) An OWL2 ontology for representing and semantically annotating pairwise and multiple sequence alignments. True False https://benhid.com/SALON/ doi:10.1186/s12859-023-05190-7 [B2AI_STANDARD:867](DataStandardOrTool.markdown) BiomedicalStandard GCS Glasgow Coma Scale Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [diagnosticinstrument] [[B2AI_TOPIC:4]](DataTopic.markdown) A neurological assessment tool used to evaluate level of consciousness based on patient responses in three categories: eye-opening, verbal response, and motor response, with a higher score indicating a more favorable neurological status. True False https://www.glasgowcomascale.org/ doi:10.1016/s0140-6736(74)91639-0 2023-05-23 -[B2AI_STANDARD:868](DataStandardOrTool.markdown) DataStandard Frictionless Frictionless data standards Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel] [[B2AI_TOPIC:5]](DataTopic.markdown) A set of patterns for describing data, including Table Schema (for tables), Data Resource (for files), and Data Package (for datasets). True False https://specs.frictionlessdata.io/ https://github.com/frictionlessdata/specs 2023-05-23 +[B2AI_STANDARD:868](DataStandardOrTool.markdown) DataStandard Frictionless Frictionless data standards Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [datamodel|has_ai_application] [[B2AI_TOPIC:5]](DataTopic.markdown) A set of patterns for describing data, including Table Schema (for tables), Data Resource (for files), and Data Package (for datasets). True False https://specs.frictionlessdata.io/ https://github.com/frictionlessdata/specs 2023-05-23 [B2AI_STANDARD:869](DataStandardOrTool.markdown) SoftwareOrTool Compass Rose Epic Compass Rose module Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:29]](DataTopic.markdown) Care coordination module focused on social determinant of health factors. Part of the Epic EHR platform. False True https://www.epic.com/software/population-health [[B2AI_ORG:105]](Organization.markdown) 2023-06-20 [B2AI_STANDARD:870](DataStandardOrTool.markdown) SoftwareOrTool GX Great Expectations platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) A platform for organizing, testing, and validating data. True False https://greatexpectations.io/ https://github.com/great-expectations/great_expectations 2023-06-20 [B2AI_STANDARD:871](DataStandardOrTool.markdown) SoftwareOrTool Pinecone Pinecone vector database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 [[B2AI_TOPIC:5]](DataTopic.markdown) A database platform built around creating vector representations of data. The basic implementation is a managed, cloud-native product, though there is a free tier. False True https://www.pinecone.io/ 2023-06-20 @@ -875,7 +875,7 @@ id category name description contributor_name contributor_github_name contributo [B2AI_STANDARD:874](DataStandardOrTool.markdown) SoftwareOrTool GGIR GGIR accelerometry package Harry Caufield caufieldjh 0000-0001-5705-7831 [[B2AI_TOPIC:18]](DataTopic.markdown) An R package to process multi-day raw accelerometer data for physical activity and sleep research. True False https://cran.r-project.org/web/packages/GGIR/vignettes/GGIR.html https://github.com/wadpac/GGIR 2023-09-25 [B2AI_STANDARD:875](DataStandardOrTool.markdown) BiomedicalStandard Badawy et al. 2019 Metadata Concepts for Advancing the Use of Digital Health Technologies in Clinical Research Harry Caufield caufieldjh 0000-0001-5705-7831 [[B2AI_TOPIC:18]](DataTopic.markdown) A proposed metadata set for digital health studies. True False https://figshare.com/articles/dataset/Supplementary_Material_for_Metadata_Concepts_for_Advancing_the_Use_of_Digital_Health_Technologies_in_Clinical_Research/9944303 doi:10.1159/000502951 2023-09-25 [B2AI_STANDARD:876](DataStandardOrTool.markdown) BiomedicalStandard GSCID/BRC CMS v1.5 GSCID/BRC Clinical Metadata Standard Harry Caufield caufieldjh 0000-0001-5705-7831 A general standard for clinical metadata. True False https://www.niaid.nih.gov/research/clinical-metadata-standard [[B2AI_ORG:118]](Organization.markdown) 2023-09-25 -[B2AI_STANDARD:877](DataStandardOrTool.markdown) BiomedicalStandard MI-CLAIM Minimum information about clinical artificial intelligence modeling Harry Caufield caufieldjh 0000-0001-5705-7831 [minimuminformationschema] A schema designed to allow rapid replication of the technical design process of a clinical AI study. True False https://github.com/beaunorgeot/MI-CLAIM doi:10.1038/s41591-020-1041-y 2023-09-25 +[B2AI_STANDARD:877](DataStandardOrTool.markdown) BiomedicalStandard MI-CLAIM Minimum information about clinical artificial intelligence modeling Harry Caufield caufieldjh 0000-0001-5705-7831 [minimuminformationschema|has_ai_application] A schema designed to allow rapid replication of the technical design process of a clinical AI study. True False https://github.com/beaunorgeot/MI-CLAIM doi:10.1038/s41591-020-1041-y 2023-09-25 [B2AI_STANDARD:878](DataStandardOrTool.markdown) DataStandardOrTool CSVW CSV on the Web Harry Caufield caufieldjh 0000-0001-5705-7831 A standard for describing and clarifying the content of CSV tables. True False https://csvw.org/ https://w3c.github.io/csvw/syntax/ 2023-09-25 [B2AI_STANDARD:879](DataStandardOrTool.markdown) DataStandardOrTool BagIt BagIt file packaging format Harry Caufield caufieldjh 0000-0001-5705-7831 A set of hierarchical file layout conventions for storage and transfer of arbitrary digital content. True False https://datatracker.ietf.org/doc/rfc8493/ doi:10.17487/RFC8493 2023-09-25 -[B2AI_STANDARD:880](DataStandardOrTool.markdown) DataStandardOrTool Unity Catalog Unity Catalog Harry Caufield caufieldjh 0000-0001-5705-7831 A universal catalog for data and AI True False https://www.unitycatalog.io/ https://github.com/unitycatalog/unitycatalog 2024-11-02 +[B2AI_STANDARD:880](DataStandardOrTool.markdown) DataStandardOrTool Unity Catalog Unity Catalog Harry Caufield caufieldjh 0000-0001-5705-7831 [has_ai_application] A universal catalog for data and AI True False https://www.unitycatalog.io/ https://github.com/unitycatalog/unitycatalog 2024-11-02 diff --git a/src/b2ai-standards-registry/datamodel/standards_schema_all.py b/src/b2ai-standards-registry/datamodel/standards_schema_all.py index 5e7d21d..f2186cb 100644 --- a/src/b2ai-standards-registry/datamodel/standards_schema_all.py +++ b/src/b2ai-standards-registry/datamodel/standards_schema_all.py @@ -1,5 +1,5 @@ # Auto generated from standards_schema_all.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-03-29T17:14:34 +# Generation date: 2024-11-04T17:40:51 # Schema: standards-schema-all # # id: https://w3id.org/bridge2ai/standards-schema-all @@ -39,9 +39,13 @@ B2AI_TOPIC = CurieNamespace('B2AI_TOPIC', 'https://w3id.org/bridge2ai/standards-datatopic-schema/') B2AI_USECASE = CurieNamespace('B2AI_USECASE', 'https://w3id.org/bridge2ai/standards-usecase-schema/') MESH = CurieNamespace('MESH', 'http://id.nlm.nih.gov/mesh/') +RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') +NCIT = CurieNamespace('ncit', 'http://purl.obolibrary.org/obo/NCIT_') RDFS = CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#') SCHEMA = CurieNamespace('schema', 'http://schema.org/') +UBERON = CurieNamespace('uberon', 'http://purl.obolibrary.org/obo/uberon/core#') +WIKIDATA = CurieNamespace('wikidata', 'http://www.wikidata.org/wiki/') XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#') DEFAULT_ = CurieNamespace('', 'https://w3id.org/bridge2ai/standards-schema-all/') @@ -100,6 +104,10 @@ class NamedThingId(URIorCURIE): pass +class AnatomicalEntityId(NamedThingId): + pass + + class DataStandardOrToolId(NamedThingId): pass @@ -217,6 +225,29 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) +@dataclass +class AnatomicalEntity(NamedThing): + """ + A subcellular location, cell type or gross anatomical part + """ + _inherited_slots: ClassVar[List[str]] = ["subclass_of", "related_to"] + + class_class_uri: ClassVar[URIRef] = B2AI.AnatomicalEntity + class_class_curie: ClassVar[str] = "B2AI:AnatomicalEntity" + class_name: ClassVar[str] = "AnatomicalEntity" + class_model_uri: ClassVar[URIRef] = URIRef("https://w3id.org/bridge2ai/standards-schema-all/AnatomicalEntity") + + id: Union[str, AnatomicalEntityId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, AnatomicalEntityId): + self.id = AnatomicalEntityId(self.id) + + super().__post_init__(**kwargs) + + @dataclass class DataStandardOrTool(NamedThing): """ @@ -592,7 +623,7 @@ class DataTopic(NamedThing): """ Represents a general data topic for Bridge2AI data or the tools/standards applied to the data. """ - _inherited_slots: ClassVar[List[str]] = ["subclass_of", "related_to"] + _inherited_slots: ClassVar[List[str]] = ["subclass_of", "related_to", "topic_involves_anatomy"] class_class_uri: ClassVar[URIRef] = B2AI_TOPIC.DataTopic class_class_curie: ClassVar[str] = "B2AI_TOPIC:DataTopic" @@ -603,6 +634,7 @@ class DataTopic(NamedThing): edam_id: Optional[Union[str, EdamIdentifier]] = None mesh_id: Optional[Union[str, MeshIdentifier]] = None ncit_id: Optional[Union[str, NcitIdentifier]] = None + topic_involves_anatomy: Optional[Union[Union[str, AnatomicalEntityId], List[Union[str, AnatomicalEntityId]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -619,6 +651,10 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.ncit_id is not None and not isinstance(self.ncit_id, NcitIdentifier): self.ncit_id = NcitIdentifier(self.ncit_id) + if not isinstance(self.topic_involves_anatomy, list): + self.topic_involves_anatomy = [self.topic_involves_anatomy] if self.topic_involves_anatomy is not None else [] + self.topic_involves_anatomy = [v if isinstance(v, AnatomicalEntityId) else AnatomicalEntityId(v) for v in self.topic_involves_anatomy] + super().__post_init__(**kwargs) @@ -897,6 +933,8 @@ class StandardsCollectionTag(EnumDefinitionImpl): description="Speech Data") standardsregistry = PermissibleValue(text="standardsregistry", description="Standards Registry") + has_ai_application = PermissibleValue(text="has_ai_application", + description="Has a direct AI application, defined as standards/tools that are: associated with ML or neural networks; schemas, or have schemas; data models; associated with DICOM; associated with AI; associated with standards used within Bridge2AI") _defn = EnumDefinition( name="StandardsCollectionTag", @@ -989,6 +1027,9 @@ class slots: slots.is_open = Slot(uri=B2AI_STANDARD.is_open, name="is_open", curie=B2AI_STANDARD.curie('is_open'), model_uri=DEFAULT_.is_open, domain=NamedThing, range=Optional[Union[bool, Bool]]) +slots.use_conditions = Slot(uri=B2AI_STANDARD.use_conditions, name="use_conditions", curie=B2AI_STANDARD.curie('use_conditions'), + model_uri=DEFAULT_.use_conditions, domain=NamedThing, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]]) + slots.requires_registration = Slot(uri=B2AI_STANDARD.requires_registration, name="requires_registration", curie=B2AI_STANDARD.curie('requires_registration'), model_uri=DEFAULT_.requires_registration, domain=NamedThing, range=Optional[Union[bool, Bool]]) @@ -1025,6 +1066,9 @@ class slots: slots.data_topics_collection = Slot(uri=B2AI_TOPIC.data_topics_collection, name="data_topics_collection", curie=B2AI_TOPIC.curie('data_topics_collection'), model_uri=DEFAULT_.data_topics_collection, domain=None, range=Optional[Union[Dict[Union[str, DataTopicId], Union[dict, DataTopic]], List[Union[dict, DataTopic]]]]) +slots.topic_involves_anatomy = Slot(uri=B2AI_TOPIC.topic_involves_anatomy, name="topic_involves_anatomy", curie=B2AI_TOPIC.curie('topic_involves_anatomy'), + model_uri=DEFAULT_.topic_involves_anatomy, domain=DataTopic, range=Optional[Union[Union[str, AnatomicalEntityId], List[Union[str, AnatomicalEntityId]]]]) + slots.ror_id = Slot(uri=B2AI_ORG.ror_id, name="ror_id", curie=B2AI_ORG.curie('ror_id'), model_uri=DEFAULT_.ror_id, domain=None, range=Optional[Union[str, RorIdentifier]]) diff --git a/src/data/DataStandardOrTool.yaml b/src/data/DataStandardOrTool.yaml index cb3b6ae..5046305 100644 --- a/src/data/DataStandardOrTool.yaml +++ b/src/data/DataStandardOrTool.yaml @@ -51,6 +51,7 @@ data_standardortools_collection: description: Access to Biological Collections Data Schema collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:1 has_relevant_organization: @@ -163,6 +164,8 @@ data_standardortools_collection: name: AIM category: BiomedicalStandard description: Annotation and Image Markup schema + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:9 - B2AI_TOPIC:15 @@ -191,6 +194,7 @@ data_standardortools_collection: Trustworthiness collection: - guidelines + - has_ai_application has_relevant_organization: - B2AI_ORG:4 purpose_detail: @@ -281,6 +285,7 @@ data_standardortools_collection: description: Argonaut Data Query Implementation Guide collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:4 has_relevant_organization: @@ -502,6 +507,7 @@ data_standardortools_collection: description: Biolink Model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:20 has_relevant_organization: @@ -642,6 +648,7 @@ data_standardortools_collection: description: BioXSD collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:20 has_relevant_organization: @@ -663,6 +670,7 @@ data_standardortools_collection: description: Brain Imaging Data Structure collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:22 purpose_detail: @@ -957,6 +965,7 @@ data_standardortools_collection: description: CDISC Laboratory Data Model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:4 has_relevant_organization: @@ -978,6 +987,7 @@ data_standardortools_collection: description: CDISC Operational Data Model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:4 has_relevant_organization: @@ -1154,6 +1164,7 @@ data_standardortools_collection: description: ClinGen Interpretation Model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:4 - B2AI_TOPIC:35 @@ -1265,6 +1276,7 @@ data_standardortools_collection: description: Collaborative Computing Project for the NMR community data model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: @@ -1288,6 +1300,7 @@ data_standardortools_collection: description: Common Fund Data Ecosystem Crosscut Metadata Model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 has_relevant_organization: @@ -1605,6 +1618,7 @@ data_standardortools_collection: collection: - audiovisual - fileformat + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1645,6 +1659,8 @@ data_standardortools_collection: name: DICOM Part 12 category: BiomedicalStandard description: DICOM Part 12 Media Formats and Physical Media for Media Interchange + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1666,6 +1682,8 @@ data_standardortools_collection: name: DICOM Part 14 category: BiomedicalStandard description: DICOM Part 14 Grayscale Standard Display Function + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1689,6 +1707,8 @@ data_standardortools_collection: name: DICOM Part 15 category: BiomedicalStandard description: DICOM Part 15 Security and System Management Profiles + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1710,6 +1730,8 @@ data_standardortools_collection: name: DCMR category: BiomedicalStandard description: DICOM Part 16 Content Mapping Resource + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1729,6 +1751,8 @@ data_standardortools_collection: name: DICOM Part 17 category: BiomedicalStandard description: DICOM Part 17 Explanatory Information + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1747,6 +1771,8 @@ data_standardortools_collection: name: DICOMweb category: BiomedicalStandard description: DICOM Part 18 Web Services + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1768,6 +1794,8 @@ data_standardortools_collection: name: DICOM Part 19 category: BiomedicalStandard description: DICOM Part 19 Application Hosting + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1793,6 +1821,8 @@ data_standardortools_collection: name: DICOM Part 2 category: BiomedicalStandard description: DICOM Part 2 Conformance + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1814,6 +1844,8 @@ data_standardortools_collection: name: DICOM Part 20 category: BiomedicalStandard description: DICOM Part 20 Imaging Reports using HL7 Clinical Document Architecture + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1835,6 +1867,8 @@ data_standardortools_collection: name: DICOM Part 21 category: BiomedicalStandard description: DICOM Part 21 Transformations between DICOM and other Representations + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1853,6 +1887,8 @@ data_standardortools_collection: name: DICOM Part 22 category: BiomedicalStandard description: DICOM Part 22 Real-Time Communication + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1873,6 +1909,8 @@ data_standardortools_collection: name: DICOM Part 3 category: BiomedicalStandard description: DICOM Part 3 Information Object Definitions + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1895,6 +1933,8 @@ data_standardortools_collection: name: DICOM Part 4 category: BiomedicalStandard description: DICOM Part 4 Service Class Specifications + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1914,6 +1954,8 @@ data_standardortools_collection: name: DICOM Part 5 category: BiomedicalStandard description: DICOM Part 5 Data Structures and Encoding + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1936,6 +1978,8 @@ data_standardortools_collection: name: DICOM Part 6 category: BiomedicalStandard description: DICOM Part 6 Data Dictionary + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1958,6 +2002,8 @@ data_standardortools_collection: name: DIMSE category: BiomedicalStandard description: DICOM Part 7 Message Exchange + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -1978,6 +2024,8 @@ data_standardortools_collection: name: DICOM Part 8 category: BiomedicalStandard description: DICOM Part 8 Network Communication Support for Message Exchange + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -2000,6 +2048,8 @@ data_standardortools_collection: name: DICOM category: BiomedicalStandard description: Digital Imaging And Communications In Medicine + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -2600,6 +2650,7 @@ data_standardortools_collection: description: Functional Genomics Experiment model for flow cytometry collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:13 purpose_detail: @@ -3920,6 +3971,7 @@ data_standardortools_collection: description: MEDIN Discovery Metadata Standard collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:11 purpose_detail: @@ -4600,6 +4652,7 @@ data_standardortools_collection: description: NCBI BioProject XML Schema collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:1 has_relevant_organization: @@ -4672,6 +4725,7 @@ data_standardortools_collection: description: Neuroimaging Data Model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:22 has_relevant_organization: @@ -4908,6 +4962,7 @@ data_standardortools_collection: description: Observational Medical Outcomes Partnership Common Data Model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:4 has_relevant_organization: @@ -4930,6 +4985,7 @@ data_standardortools_collection: description: Observational Medical Outcomes Partnership Common Evidence Model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:4 has_relevant_organization: @@ -5061,6 +5117,7 @@ data_standardortools_collection: description: openEHR Archetype Object Model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:9 has_relevant_organization: @@ -5186,6 +5243,7 @@ data_standardortools_collection: description: Phenopackets schema collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:4 has_relevant_organization: @@ -5576,6 +5634,7 @@ data_standardortools_collection: description: Sentinel Common Data Model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:9 has_relevant_organization: @@ -5612,6 +5671,7 @@ data_standardortools_collection: description: Sequence Read Archive Metadata XML collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:12 - B2AI_TOPIC:13 @@ -5690,6 +5750,7 @@ data_standardortools_collection: description: SPDI data model collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:12 - B2AI_TOPIC:13 @@ -6004,6 +6065,7 @@ data_standardortools_collection: description: Taxonomic Concept Transfer Schema collection: - datamodel + - has_ai_application has_relevant_organization: - B2AI_ORG:93 purpose_detail: @@ -7180,6 +7242,7 @@ data_standardortools_collection: description: Neural Network Exchange Format collection: - fileformat + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: @@ -7242,6 +7305,7 @@ data_standardortools_collection: description: Open Neural Network Exchange collection: - fileformat + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: ONNX is an open format built to represent machine learning models. @@ -8143,6 +8207,8 @@ data_standardortools_collection: name: AIO category: OntologyOrVocabulary description: Artificial Intelligence Ontology + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: General terms for AI @@ -9271,6 +9337,8 @@ data_standardortools_collection: name: ITO category: OntologyOrVocabulary description: Intelligence Task Ontology + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 has_relevant_organization: @@ -12911,6 +12979,8 @@ data_standardortools_collection: name: Gupta2021 category: ReferenceImplementation description: A DICOM Standard Pipeline for Microscope Imaging Modalities + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:19 has_relevant_organization: @@ -12999,6 +13069,8 @@ data_standardortools_collection: description: Design and Implementation of the Pre-Clinical DICOM Standard in Multi-Cohort Murine Studies + collection: + - has_ai_application concerns_data_topic: - B2AI_TOPIC:15 has_relevant_organization: @@ -13255,6 +13327,8 @@ data_standardortools_collection: Towards Clinical Practice - Design and Implementation of Convolutional Neural Network-Based Assistive Diagnosis System for COVID-19 Case Detection from Chest X-Ray Images + collection: + - has_ai_application has_relevant_organization: - B2AI_ORG:25 purpose_detail: @@ -13372,6 +13446,7 @@ data_standardortools_collection: description: Bridge to Artificial Intelligence Registry collection: - standardsregistry + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: Standards, tools, reference implementations, and related resources. @@ -13628,6 +13703,7 @@ data_standardortools_collection: description: Aesara collection: - machinelearningframework + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: @@ -14048,6 +14124,7 @@ data_standardortools_collection: description: Contextual Ontology-based Repository Analysis Library collection: - datamodel + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: @@ -14231,6 +14308,7 @@ data_standardortools_collection: description: Determined collection: - machinelearningframework + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: Determined is an open-source deep learning training platform. @@ -14392,6 +14470,7 @@ data_standardortools_collection: description: FastAI collection: - machinelearningframework + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: @@ -14454,6 +14533,7 @@ data_standardortools_collection: collection: - graphdataplatform - machinelearningframework + - has_ai_application concerns_data_topic: - B2AI_TOPIC:21 purpose_detail: @@ -14525,6 +14605,7 @@ data_standardortools_collection: description: Holistic AI in Medicine framework collection: - multimodal + - has_ai_application purpose_detail: A unified Holistic AI in Medicine (HAIM) framework to facilitate the generation and testing of AI systems that leverage multimodal inputs. @@ -14809,6 +14890,7 @@ data_standardortools_collection: description: Medical Open Network for AI collection: - machinelearningframework + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: @@ -14916,6 +14998,7 @@ data_standardortools_collection: description: MLPro framework collection: - machinelearningframework + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: @@ -15136,6 +15219,7 @@ data_standardortools_collection: description: NeuCA - Neural-network based Cell Annotation tool collection: - scrnaseqanalysis + - has_ai_application concerns_data_topic: - B2AI_TOPIC:34 purpose_detail: @@ -15312,6 +15396,7 @@ data_standardortools_collection: description: PyTorch collection: - machinelearningframework + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: A popular machine learning platform. @@ -15385,6 +15470,7 @@ data_standardortools_collection: description: Relexi collection: - machinelearningframework + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: @@ -15582,6 +15668,7 @@ data_standardortools_collection: description: Tensorflow collection: - machinelearningframework + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 has_relevant_organization: @@ -15634,6 +15721,7 @@ data_standardortools_collection: collection: - deprecated - machinelearningframework + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: @@ -15786,6 +15874,7 @@ data_standardortools_collection: description: ZenML collection: - machinelearningframework + - has_ai_application concerns_data_topic: - B2AI_TOPIC:5 purpose_detail: @@ -16228,6 +16317,7 @@ data_standardortools_collection: requires_registration: false collection: - datamodel + - has_ai_application url: https://specs.frictionlessdata.io/ formal_specification: https://github.com/frictionlessdata/specs contributor_name: Harry Caufield @@ -16369,6 +16459,7 @@ data_standardortools_collection: description: Minimum information about clinical artificial intelligence modeling collection: - minimuminformationschema + - has_ai_application purpose_detail: A schema designed to allow rapid replication of the technical design process of a clinical AI study. is_open: true requires_registration: false @@ -16408,6 +16499,8 @@ data_standardortools_collection: category: DataStandardOrTool name: Unity Catalog description: Unity Catalog + collection: + - has_ai_application purpose_detail: A universal catalog for data and AI is_open: true requires_registration: false diff --git a/src/schema/standards_datastandardortool_schema.yaml b/src/schema/standards_datastandardortool_schema.yaml index abd2f4e..7df3dbc 100644 --- a/src/schema/standards_datastandardortool_schema.yaml +++ b/src/schema/standards_datastandardortool_schema.yaml @@ -71,7 +71,7 @@ classes: A set of concepts and categories, potentially defined or accompanied by their hierarchical relationships. - + ModelRepository: is_a: DataStandardOrTool description: >- @@ -86,7 +86,7 @@ classes: Represents a resource in the Bridge2AI Standards Registry serving as a standardized, reusable data source. - + SoftwareOrTool: is_a: DataStandardOrTool description: >- @@ -122,20 +122,30 @@ slots: description: >- Tags for specific sets of standards. multivalued: true - + purpose_detail: range: string is_a: node_property description: >- Text description of the standard or tool. - + is_open: is_a: node_property range: boolean description: >- Is the standard or tool FAIR and available free of cost? - + + use_conditions: + is_a: node_property + range: uriorcurie + multivalued: true + values_from: + - DUO + description: >- + Applicable conditions on use, as defined + by the Data Use Ontology (DUO). + requires_registration: is_a: node_property range: boolean @@ -151,7 +161,7 @@ slots: in the context of object data topic. domain: DataStandardOrTool range: DataTopic - + publication: is_a: node_property range: uriorcurie @@ -261,4 +271,12 @@ enums: description: Speech Data standardsregistry: description: Standards Registry - + has_ai_application: + description: >- + Has a direct AI application, defined as standards/tools that are: + associated with ML or neural networks; + schemas, or have schemas; + data models; + associated with DICOM; + associated with AI; + associated with standards used within Bridge2AI