diff --git a/code/createPage.py b/code/createPage.py index 24e42d6..ec9db94 100644 --- a/code/createPage.py +++ b/code/createPage.py @@ -2,10 +2,11 @@ import json import subprocess import shutil +import traceback DOCS_SUBFOLDERS = ['consortia', 'projects', 'theses'] RO_CRATE_SUBFOLDERS = ['projects', 'theses'] -MAPPINGS = [("employee", "Current project members"), ("alumni", "Previous project members"), ("alternativeHeadline", "Cite as"), ("citation", "Cite as"), ("member", "External contributors"), ("knowsAbout", "Outcomes"), ("parentOrganization", "Parent organization, consortium or research project"), ("subOrganization", "Sub-projects")] +MAPPINGS = [("employee", "Current project members"), ("alumni", "Previous project members"), ("alternativeHeadline", "Cite as"), ("citation", "Cite as"), ("member", "External contributors"), ("knowsAbout", "Outcomes"), ("parentOrganization", "Parent organization, consortium or research project"), ("subOrganization", "Sub-projects"), ("targetproduct", "Release")] MAPPINGS_FROM = [i[0] for i in MAPPINGS] MAPPINGS_TO = [i[1] for i in MAPPINGS] @@ -284,12 +285,52 @@ def processNamesInProject(item) : subTypeURL = item["@type"] idURL = item["@id"] md += f'Visit URL Visit {subTypeURL}\n\n' - for prop, val in item.items(): - if prop not in ["@type", "@id", "name", "http://purl.org/dc/terms/conformsTo", "funder", "givenName", "familyName"]: - if prop == 'url': - md += renderUrlAsHref(val) - else : - md += f'- {prop.capitalize()}: {val}\n' + if isinstance(item, (dict)): + for prop, val in item.items(): + if prop not in ["@type", "@id", "name", "http://purl.org/dc/terms/conformsTo", "funder", "givenName", "familyName"]: + if prop == 'url': + md += renderUrlAsHref(val) + elif prop == 'license': + try: + idURL = val["@id"] + md += f'- License: {idURL} \n' + except: + md += f'- License: {val}\n' + elif (prop == 'author'): + try: + if isinstance(val, list): + md += f'- {prop.capitalize()}s: ' + for elem in val: + idURL = elem["@id"] + md += f'{idURL}. ' + md += '\n' + else: + md += f'- {prop.capitalize()}: ' + idURL = val["@id"] + md += f'{idURL} \n' + except: + pass + elif (prop == 'targetProduct'): + try: + if isinstance(val, list): + md += f'- Releases: ' + for elem in val: + idURL = elem["@id"] + md += f'{idURL}. ' + md += '\n' + else: + md += f'- Release: ' + idURL = val["@id"] + md += f'{idURL} \n' + except: + pass + else : + if prop in MAPPINGS_FROM : + i = MAPPINGS_FROM.index(prop) + md += f'- {MAPPINGS_TO[i]}: ' + else : + md += f'- {prop.capitalize()}: ' + md += f'{val}\n' return md def processProjectData(data, jsonFileURL, rocrateFileURL, htmlFileURL): @@ -324,10 +365,9 @@ def processProjectData(data, jsonFileURL, rocrateFileURL, htmlFileURL): if isinstance(item, (dict, list)): #each item is an object/dict #loop on each key, value pair - for mdFolderName in item: - subItem = item.get(mdFolderName, "") - if (isinstance(subItem,(dict, list))): - md += processNamesInProject(subItem) + #for keyPair in item: + # valuePair = item.get(keyPair, "") + # md += processKeyValuePair(keyPair, valuePair) md += processNamesInProject(item) elif isinstance(value, dict): for subProperty, subValue in value.items(): @@ -437,6 +477,7 @@ def fromMetadatatoDocs(): folderIndex = DOCS_SUBFOLDERS.index(mdFolderName) jsonFileURL = f"../../metadata/{mdFolderName}/{fileNameNoExt}.json" rocrateFileURL = "" + htmlFileURL = "" if mdFolderName in RO_CRATE_SUBFOLDERS: rocrateFileURL = f"../../metadata/{mdFolderName}/{fileNameNoExt}/ro-crate-metadata.json" htmlFileURL = f"../../metadata/{mdFolderName}/{fileNameNoExt}/ro-crate-preview.html" @@ -447,7 +488,9 @@ def fromMetadatatoDocs(): mdDocFile.write(md) mdDocFile.write(f'\n\n\n\n') except Exception as e: - #print(e) + print(jsonFileName) + print(e) + #print(traceback.format_exc()) jsonFileURL = f"../metadata/{mdFolderName}/{fileNameNoExt}.json" md = generateMDTableFromJSON(data, jsonFileURL) with open(docFilePath, "a", encoding="utf-8") as mdDocFile: diff --git a/docs/consortia/2018_STELLA.md b/docs/consortia/2018_STELLA.md index 9c86f7f..76b3f59 100644 --- a/docs/consortia/2018_STELLA.md +++ b/docs/consortia/2018_STELLA.md @@ -45,20 +45,15 @@ Evaluation framework, A/B testing, Interlinking, Information Retrieval, Recommen #### OntoClue -Visit URL Visit ResearchProject +Visit URL Visit ResearchProject #### TREC document-to-document relevance assessment -Visit URL Visit ResearchProject +Visit URL Visit ResearchProject ### Funding -#### Deutsche Forschungsgemeinschaft - -Visit URL Visit Organization - -- Alternatename: German Research Foundation -- URL: http://www.dfg.de/en/ +Visit URL Visit Grant - Identifier: 407518790 - Description: Project no. 407518790 (corresponding to the STELLA project) @@ -107,18 +102,19 @@ Evaluation framework, A/B testing, Interlinking, Information Retrieval, Recommen "subOrganization": [ { "@type": "ResearchProject", - "@id": "https://zbmed-semtec.github.io/projects/2021_OntoClue", + "@id": "https://w3id.org/zbmed-semtec/projects/2021_OntoClue", "name": "OntoClue" }, { "@type": "ResearchProject", - "@id": "https://zbmed-semtec.github.io/projects/2022_TREC_doc2doc", + "@id": "https://w3id.org/zbmed-semtec/projects/2022_TREC_doc2doc", "name": "TREC document-to-document relevance assessment" } ], "funding": [ { "@type": "Grant", + "@id": "https://gepris.dfg.de/gepris/projekt/407518790", "funder": { "@type": "Organization", "@id": "https://ror.org/018mejw64", diff --git a/docs/consortia/2021_NFDI4DataScience.md b/docs/consortia/2021_NFDI4DataScience.md index 0b7d7b4..164055c 100644 --- a/docs/consortia/2021_NFDI4DataScience.md +++ b/docs/consortia/2021_NFDI4DataScience.md @@ -34,13 +34,6 @@ NFDI, Data Science, Artificial Intelligence ### Funding -#### Deutsche Forschungsgemeinschaft - -Visit URL Visit Organization - -- Alternatename: German Research Foundation -- URL: http://www.dfg.de/en/ - Visit URL Visit Grant - Identifier: 460234259 diff --git a/docs/current_members.md b/docs/current_members.md index 91a06e3..be2c152 100644 --- a/docs/current_members.md +++ b/docs/current_members.md @@ -90,36 +90,6 @@ } -### Sarker Sunzid Mahmud -

Get JSON-LD Get JSON-LD | Visit URL Visit Person

- - - - - - - - - - - - - - - -
familyNameMahmud
givenNameSarker Sunzid
jobTitleStudent assistant
- - - ### Nelson Quiñones

Get JSON-LD Get JSON-LD | Visit URL Visit Person

diff --git a/docs/metadata/projects/2021_OntoClue.json b/docs/metadata/projects/2021_OntoClue.json index a7e2079..3246181 100644 --- a/docs/metadata/projects/2021_OntoClue.json +++ b/docs/metadata/projects/2021_OntoClue.json @@ -176,6 +176,13 @@ "alternativeHeadline": "Ravinder R, Fellerhof T, Dadi V, Geist L, Talha M, Rebholz-Schuhmann D, et al. A Comparison of Vector-based Approaches for Document Similarity Using the RELISH Corpus. Proceedings of the 6th Workshop on Semantic Web Solutions for Large-Scale Biomedical Data Analytics co-located with ESWC 2023. CEUR; 2023. Available: https://ceur-ws.org/Vol-3466/paper5.pdf", "name": "A Comparison of Vector-based Approaches for Document Similarity Using the RELISH Corpus", "datePublished": "2023-03-01", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://ceur-ws.org/Vol-3466/paper5.pdf#", "author": [ {"@id": "https://orcid.org/0009-0004-4484-6283"}, @@ -196,6 +203,13 @@ "citation": "Ravinder R, Fellerhoff T, Dadi VV, Geist L, Rocamora G, Talha M, et al. OntoClue, a framework to compare vector-based approaches for document relatedness using the RELISH corpus - Poster. ZB MED - Informationszentrum Lebenswissenschaften; 2023. Available: https://repository.publisso.de/resource/frl:6440397", "name": "OntoClue, a framework to compare vector-based approaches for document relatedness using the RELISH corpus", "datePublished": "2023-06-22", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://repository.publisso.de/resource/frl:6440397", "author": [ {"@id": "https://orcid.org/0009-0004-4484-6283"}, @@ -215,6 +229,13 @@ "alternativeHeadline": "Ravinder R, Fellerhoff T, Dadi V, Geist L, Rocamora G, Talha M, et al. OntoClue, a framework to compare vector-based approaches for document relatedness using the RELISH corpus. CEUR; 2023. Available: https://ceur-ws.org/Vol-3415/paper-38.pdf", "name": "OntoClue, a framework to compare vector-based approaches for document relatedness using the RELISH corpus - Poster", "datePublished": "2023-03-01", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://ceur-ws.org/Vol-3415/paper-38.pdf#", "author": [ {"@id": "https://orcid.org/0009-0004-4484-6283"}, @@ -235,6 +256,14 @@ "alternativeHeadline": "Ritchie A, Chen J, Castro LJ, Rebholz-Schuhmann D, Jimenez-Ruiz E. Ontology Clustering with OWL2Vec*. CEUR Workshop Proceedings. Online: CEUR Workshop Proceedings; 2021. Available: http://ceur-ws.org/", "name": "Ontology Clustering with OWL2Vec*", "datePublished": "2021-07-28", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, + "url": "https://ceur-ws.org/Vol-2918/short3.pdf#", "author": [ {"@id": "https://zbmed-semtec.github.io/previous_members/#ashley-ritchie"}, {"@id": "https://chenjiaoyan.github.io/"}, diff --git a/docs/metadata/projects/2022_TREC_doc2doc.json b/docs/metadata/projects/2022_TREC_doc2doc.json index 8ba9da6..c9b3cff 100644 --- a/docs/metadata/projects/2022_TREC_doc2doc.json +++ b/docs/metadata/projects/2022_TREC_doc2doc.json @@ -110,8 +110,16 @@ "@id": "https://ceur-ws.org/Vol-3415/paper-12.pdf", "http://purl.org/dc/terms/conformsTo": "https://bioschemas.org/profiles/ScholarlyArticle/0.3-DRAFT", "identifier": "CEUR:Vol-3415/paper-12", + "alternativeHeadline": "Giraldo O, Cadena MF, Robayo-Gama A, Solanki D, Fellerhoff T, Geist L, et al. Document-to-document relevance assessment for TREC Genomics Track 2005. CEUR; 2023. Available: https://ceur-ws.org/Vol-3415/paper-12.pdf", "name": "Document-to-document relevance assessment for TREC Genomics Track 2005", "datePublished": "2023-06-22", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://ceur-ws.org/Vol-3415/paper-12.pdf#", "author": [ {"@id": "https://orcid.org/0000-0003-2978-8922"}, @@ -129,11 +137,19 @@ "@type": "SoftwareApplication", "@id": "https://doi.org/10.5281/zenodo.7341391", "http://purl.org/dc/terms/conformsTo": "https://bioschemas.org/profiles/ComputationalTool/1.0-RELEASE", + "identifier": "DOI:10.5281/zenodo.7341391", + "citation": "Talha M, Geist L, Fellerhof T, Ravinder R, Giraldo O, Rebholz-Schuhmann D, et al. TREC-doc-2-doc-relevance assessment interface. Zenodo; 2022. doi:10.5281/zenodo.7341391", "name": "TREC-doc-2-doc-relevance assessment interface", "description": "The code, data and docs at this release aim at facilitating the creation of a doc-2-doc relevance assessment on PMIDs used in the TREC 2005 Genomics track. A doc-2-doc relevance assessment takes one document as reference and assess a second document regarding its relevance to the reference one. This doc-2-doc collection will be used to evaluate the doc-2-doc recommendations approaches that we are working on.", "url": "https://zenodo.org/records/7341391", "softwareVersion": "1.0.0", "datePublished": "2022-11-21", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/MIT.html", + "name": "MIT License", + "url": "https://opensource.org/license/mit/" + }, "author": [ {"@id": "https://zbmed-semtec.github.io/previous_members/#muhammad-talha"}, {"@id": "http://orcid.org/0000-0002-2910-7982"}, @@ -146,10 +162,17 @@ },{ "@type": "SoftwareSourceCode", "@id": "https://github.com/zbmed-semtec/TREC-doc-2-doc-relevance", + "citation": "Talha M, Geist L, Fellerhof T, Ravinder R, Giraldo O, Rebholz-Schuhmann D, et al. TREC-doc-2-doc-relevance [Software source code]. GitHub; 2022.", "name": "TREC-doc-2-doc-relevance", "description": "This is the software source code facilitating the creation of a doc-2-doc relevance assessment on PMIDs used in the TREC 2005 Genomics track along with its metadata.", "url": "https://github.com/zbmed-semtec/TREC-doc-2-doc-relevance", "targetProduct": { "@id": "https://doi.org/10.5281/zenodo.7341391" }, + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/MIT.html", + "name": "MIT License", + "url": "https://opensource.org/license/mit/" + }, "author": [ {"@id": "https://zbmed-semtec.github.io/previous_members/#muhammad-talha"}, {"@id": "http://orcid.org/0000-0002-2910-7982"}, @@ -164,6 +187,7 @@ "@id": "https://doi.org/10.5281/zenodo.7338056", "conformsTo": "https://bioschemas.org/profiles/Dataset/1.1-DRAFT", "identifier": "DOI:10.5281/zenodo.7338056", + "citation": "Giraldo O, Solanki D, Rebholz-Schuhmann D, Castro LJ. Fleiss kappa for doc-2-doc relevance assessment. Zenodo; 2022. doi:10.5281/zenodo.7338056", "name": "Fleiss kappa for doc-2-doc relevance assessment", "description": "Fleiss' kappa measuring inter-annotator agreement on a document-to-document relevance assessment task. The table contains 7 columns, the first one presents the topics, 8 in total. The second column shows the “reference articles”, represented by their PubMed-ID and organized by topic. The third column shows the Fleiss’ Kappa results. The fourth column shows the interpretation of the Fleiss' Kappa results being: i) “Poor” results <0.20, ii) “Fair” results within 0.21 - 0.40, and iii) “Moderate” results within 0.41 - 0.60. The fifth column shows the PubMed-IDs of evaluation articles rated by the four annotators as “Relevant” regarding its corresponding “reference article”. The sixth column shows the PubMed-IDs of evaluation articles rated by the four annotators as “Partially relevant” regarding its corresponding “reference article”. The seventh column shows the PubMed-IDs of evaluation articles rated by the four annotators as “Non-relevant” regarding its corresponding “reference article”", "keywords": "Fleiss' Kappa, Inter-annoator agreement, TREC Genomics Track 2005, relevance assessment", @@ -187,6 +211,7 @@ "@id": "https://doi.org/10.5281/zenodo.7324822", "http://purl.org/dc/terms/conformsTo": "https://bioschemas.org/profiles/Dataset/1.1-DRAFT", "identifier": "DOI:10.5281/zenodo.7324822", + "citation": "Giraldo O, Solanki D, Cadena F, Robayo-Gama A, Rebholz-Schuhmann D, Castro LJ. Document-to-document relevant assessment for TREC Genomics Track 2005. Zenodo; 2022. doi:10.5281/zenodo.7324822", "name": "Document-to-document relevant assessment for TREC Genomics Track 2005", "description": "A CSV table with document-to-document relevance assessment judgements on a subset of the TREC Genomics Track 2005 produced by four annotators. The 'raw data document evaluation' contains six columns, first row consecutive id, second original TREC topic, third PubMed Id used as reference document, fourth PMID used to evaluate the relevance wrt the reference document, fifth the relevance score (2 definitely relevant, 1 partially relevant, 0 non-relevant), and sixth annotator id", "keywords": "Document-to-document relevance, TREC GEnomics Track 2005, relevance assessment", diff --git a/docs/metadata/projects/2022_maSMP.json b/docs/metadata/projects/2022_maSMP.json index 7166fd3..b6830bc 100644 --- a/docs/metadata/projects/2022_maSMP.json +++ b/docs/metadata/projects/2022_maSMP.json @@ -105,6 +105,13 @@ "citation": "Castro LJ, Giraldo O, Geist L, Quiñones N, Solanki D, Rebholz-Schuhmann D. Metadata model for machine-actionable Software Management Plans [Software source code and vocabulary]. GitHub; 2024.", "name": "Metadata model for machine-actionable Software Management Plans", "url": "https://github.com/zbmed-semtec/maSMPs#", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "author": [ {"@id": "https://orcid.org/0000-0003-3986-0510"}, {"@id": "https://orcid.org/0000-0003-2978-8922"}, @@ -122,6 +129,13 @@ "name": "machine-actionable Software Management Plan Ontology (maSMP Ontology)", "datePublished": "2024-01-29", "version": "2.1.0", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://zenodo.org/records/10582073", "author": [ {"@id": "https://orcid.org/0000-0003-3986-0510"}, @@ -140,6 +154,13 @@ "name": "Usage guidance (aka profiles) for the machine-actionable Software Management Plan Ontology", "datePublished": "2024-01-29", "version": "2.1.1", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://zenodo.org/records/10582121", "author": [ {"@id": "https://orcid.org/0000-0003-3986-0510"}, @@ -157,6 +178,13 @@ "identifier": "DOI:10.5281/zenodo.10374839", "name": "Five Minutes to Write a Software Management Plan – A Machine-actionable Approach to Simplify the Creation of SMPs", "datePublished": "2023-09-07", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://zenodo.org/records/10374839", "author":[ {"@id": "https://orcid.org/0000-0003-3986-0510"}, @@ -179,6 +207,13 @@ "alternativeHeadline": "Giraldo O, Dessi D, Dietze S, Rebholz-Schuhmann D, Castro LJ. Machine-Actionable Metadata for Software and Software Management Plans for NFDI. Proceedings of the Conference on Research Data Infrastructure. 2023. doi:10.52825/cordi.v1i.279", "name": "Machine-Actionable Metadata for Software and Software Management Plans for NFDI", "datePublished": "2023-09-07", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://www.tib-op.org/ojs/index.php/CoRDI/article/view/279", "author":[ {"@id": "https://orcid.org/0000-0003-2978-8922"}, @@ -195,6 +230,13 @@ "citation": "Giraldo O, Dessi D, Dietze S, Rebholz-Schuhmann D, Castro LJ. Machine-Actionable Metadata for Software and Software Management Plans for NFDI - Presentation. 2023 Sep 15. doi:10.5281/zenodo.8349183", "name": "Machine-Actionable Metadata for Software and Software Management Plans for NFDI - Presentation", "datePublished": "2023-09-15", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://zenodo.org/records/8349183", "author":[ {"@id": "https://orcid.org/0000-0003-2978-8922"}, @@ -211,6 +253,13 @@ "alternativeHeadline": "Giraldo O, Cardoso J, Martin del Pico E, Gaignard A, Geist L, Grossmann YV, et al. Workshop machine-actionable Software Management Plans. Zenodo; 2023 Jun. doi:10.5281/zenodo.8087357", "name": "Workshop machine-actionable Software Management Plans", "datePublished": "2023-06-27", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://zenodo.org/records/8087357", "author": [ {"@id": "https://orcid.org/0000-0003-2978-8922"}, @@ -233,6 +282,13 @@ "alternativeHeadline": "Giraldo O, Geist L, Quiñones N, Solanki D, Alves R, Bampalikis D, et al. A metadata schema for machine-actionable Software Management Plans. PUBLISSO-FRL; 2023. doi:10.4126/FRL01-006444988", "name": "A metadata schema for machine-actionable Software Management Plans", "datePublished": "2023-06-16", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://repository.publisso.de/resource/frl:6444988", "author": [ {"@id": "https://orcid.org/0000-0003-2978-8922"}, @@ -257,6 +313,13 @@ "alternativeHeadline": "Giraldo O, Alves R, Bampalikis D, Fernández JM, Martin Del Pico E, Posomopoulos F, et al. A metadata analysis for machine-actionable Software Management Plans. CEUR; 2023. Available: https://ceur-ws.org/Vol-3415/paper-31.pdf", "name": "A metadata analysis for machine-actionable Software Management Plans", "datePublished": "2023-06-22", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://ceur-ws.org/Vol-3415/paper-31.pdf#", "author": [ {"@id": "https://orcid.org/0000-0003-2978-8922"}, @@ -278,6 +341,13 @@ "citation": "Giraldo O, Alves R, Bampalikis D, Fernández González JM, Martin Del Pico E, Psomopoulos F, et al. A metadata analysis for machine-actionable Software Mng Plans - Poster. Poster presented at: SWAT4HCLS 2023; ZB MED - Informationszentrum Lebenswissenschaften; 2023. Available: https://repository.publisso.de/resource/frl:6440396", "name": "A metadata analysis for machine-actionable Software Management Plans - Poster", "datePublished": "2023-03-01", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://repository.publisso.de/resource/frl:6440396", "author": [ {"@id": "https://orcid.org/0000-0003-2978-8922"}, @@ -300,6 +370,13 @@ "alternativeHeadline": "Giraldo O, Alves R, Bampalikis D, Fernandez J, Pico EM del, Psomopoulos F, et al. A FAIRification roadmap for ELIXIR Software Management Plans. Research Ideas and Outcomes. Pensoft Publishers; 2022. p. e94608. doi:10.3897/rio.8.e94608", "name": "A FAIRification roadmap for ELIXIR Software Management Plans", "datePublished": "2022-10-12", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://riojournal.com/article/94608/", "author": [ {"@id": "https://orcid.org/0000-0003-2978-8922"}, @@ -319,6 +396,13 @@ "citation": "Giraldo O, Alves R, Bampalikis D, Fernandez JM, Pico EM del, Psomopoulos FE, et al. A FAIRification roadmap for ELIXIR Software Management Plans - Poster. 2022 Oct 25. doi:10.5281/zenodo.7249674", "name": "A FAIRification roadmap for ELIXIR Software Management Plans - Poster", "datePublished": "2022-10-25", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "url": "https://zenodo.org/records/7249674", "author": [ {"@id": "https://orcid.org/0000-0003-2978-8922"}, diff --git a/docs/metadata/theses/2023_Protein_function_embeddings.json b/docs/metadata/theses/2023_Protein_function_embeddings.json index 1cb4b99..2b271df 100644 --- a/docs/metadata/theses/2023_Protein_function_embeddings.json +++ b/docs/metadata/theses/2023_Protein_function_embeddings.json @@ -61,6 +61,13 @@ "name": "Comparative analysis of protein function text-based embeddings and its potential for prediction tasks : master thesis", "dateCreated": "2023-04-17", "url": "https://repository.publisso.de/resource/frl:6472635", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "author": {"@id": "https://orcid.org/0009-0004-4484-6283"} }, { @@ -72,7 +79,13 @@ "description": "This is the Software Source Code corresponding to the thesis along with its metadata.", "url": "https://github.com/zbmed-semtec/protein-function-embeddings-thesis#", "programmingLanguage": "Python", - "targetApplication": { "@id": "https://doi.org/10.5281/zenodo.7781869" }, + "targetProduct": { "@id": "https://doi.org/10.5281/zenodo.7781869" }, + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/GPL-3.0-only.html", + "name": "GPL-3.0-only", + "url": "https://www.gnu.org/licenses/gpl-3.0-standalone.html" + }, "author": [ {"@id": "https://orcid.org/0009-0004-4484-6283"}, {"@id": "https://orcid.org/0000-0003-3986-0510"}, @@ -90,6 +103,12 @@ "url": "https://zenodo.org/records/7781870", "softwareVersion": "v1.0.1", "datePublished": "2023-03-29", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/GPL-3.0-only.html", + "name": "GPL-3.0-only", + "url": "https://www.gnu.org/licenses/gpl-3.0-standalone.html" + }, "author": [ {"@id": "https://orcid.org/0009-0004-4484-6283"}, {"@id": "https://orcid.org/0000-0003-3986-0510"}, @@ -107,6 +126,13 @@ "url": "https://zenodo.org/records/7793384", "version": "v1.0.0" , "datePublished": "2023-04-02", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "author": [ {"@id": "https://orcid.org/0009-0004-4484-6283"}, {"@id": "https://orcid.org/0000-0003-3986-0510"}, @@ -122,6 +148,13 @@ "name": "Comparative analysis of protein function text-based embeddings and their applicability to prediction tasks", "datePublished": "2023-06-22", "url": "https://ceur-ws.org/Vol-3415/paper-21.pdf#", + "license": { + "@type": "CreativeWork", + "@id": "https://spdx.org/licenses/CC-BY-4.0.html", + "name": "Creative Commons Attribution 4.0 International", + "alternateName": "CC BY 4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, "author": [ {"@id": "https://orcid.org/0009-0004-4484-6283"}, {"@id": "https://orcid.org/0000-0003-3986-0510"}, diff --git a/docs/previous_members.md b/docs/previous_members.md index b8b62c3..3437ad9 100644 --- a/docs/previous_members.md +++ b/docs/previous_members.md @@ -200,6 +200,36 @@ } +### Sarker Sunzid Mahmud +

Get JSON-LD Get JSON-LD | Visit URL Visit Person

+
+ + + + + + + + + + + + + + +
familyNameMahmud
givenNameSarker Sunzid
jobTitleStudent assistant
+ + + ### Muhammad Talha

Get JSON-LD Get JSON-LD | Visit URL Visit Person

diff --git a/docs/projects/2021_OntoClue.md b/docs/projects/2021_OntoClue.md index afb4c73..755f7d0 100644 --- a/docs/projects/2021_OntoClue.md +++ b/docs/projects/2021_OntoClue.md @@ -12,14 +12,26 @@ OntoClue aims to provide a framework to optimize and compare document-similarity ### Keywords word-embeddings, document-embeddings, ontology-embeddings, document similarity, document relevance, doc2doc relevance, ontology enrichment +### Url + +- URL: https://zbmed-semtec.github.io/projects/2021_OntoClue + ### Current project members +- Muskaan Chopra Visit URL Visit Person + - Lukas Geist Visit URL Visit Person +- Endri Gupta Visit URL Visit Person + +- Soudeh Jahanshahi Visit URL Visit Person + - Nelson Quiñones Visit URL Visit Person - Rohitha Ravinder Visit URL Visit Person +- Suhasini Venkatesh Visit URL Visit Person + - Dietrich Rebholz-Schuhmann Visit URL Visit Person - Leyla Jael Castro Visit URL Visit Person @@ -32,6 +44,10 @@ word-embeddings, document-embeddings, ontology-embeddings, document similarity, - Georgi Lazarov Visit URL Visit Person +- Sarker Sunzid Mahmud Visit URL Visit Person + +- Ashley Ritchie Visit URL Visit Person + - Muhammad Talha Visit URL Visit Person - Guilermo Rocamora Perez Visit URL Visit Person @@ -42,7 +58,9 @@ word-embeddings, document-embeddings, ontology-embeddings, document similarity, #### Semantic Technologies team at ZB MED -Visit URL Visit ResearchOrganization +Visit URL Visit ResearchOrganization + +- URL: https://zbmed-semtec.github.io/ ### Parent organization, consortium or research project @@ -57,94 +75,98 @@ word-embeddings, document-embeddings, ontology-embeddings, document similarity, Visit URL Visit Consortium +- URL: https://www.nfdi4datascience.de/ + #### STELLA Living Labs Project Visit URL Visit ResearchProject -### Funding +- URL: https://stella-project.org -#### Deutsche Forschungsgemeinschaft - -Visit URL Visit Organization - -- Alternatename: German Research Foundation -- URL: http://www.dfg.de/en/ +### Funding Visit URL Visit Grant - Identifier: 460234259 - Description: Project no. 460234259 (corresponding to the NFDI4DataScience consortium) -#### Deutsche Forschungsgemeinschaft - -Visit URL Visit Organization - -- Alternatename: German Research Foundation -- URL: http://www.dfg.de/en/ - Visit URL Visit Grant - Identifier: 407518790 - Description: Project no. 407518790 (corresponding to the STELLA project) ### Outcomes +#### A Comparison of Vector-based Approaches for Document Similarity Using the RELISH Corpus + +Visit URL Visit ScholarlyArticle + +- Identifier: CEUR:Vol-3466/paper5 +- Cite as: Ravinder R, Fellerhof T, Dadi V, Geist L, Talha M, Rebholz-Schuhmann D, et al. A Comparison of Vector-based Approaches for Document Similarity Using the RELISH Corpus. Proceedings of the 6th Workshop on Semantic Web Solutions for Large-Scale Biomedical Data Analytics co-located with ESWC 2023. CEUR; 2023. Available: https://ceur-ws.org/Vol-3466/paper5.pdf +- Datepublished: 2023-03-01 +- License: https://spdx.org/licenses/CC-BY-4.0.html +- URL: https://ceur-ws.org/Vol-3466/paper5.pdf# + +- Authors: https://orcid.org/0009-0004-4484-6283. https://orcid.org/0000-0002-8725-1317. https://orcid.org/0000-0002-3082-7522. https://orcid.org/0000-0002-2910-7982. https://orcid.org/0000-0002-4795-3648. https://zbmed-semtec.github.io/previous_members/#muhammad-talha. https://orcid.org/0000-0002-1018-0370. https://orcid.org/0000-0003-3986-0510. #### OntoClue, a framework to compare vector-based approaches for document relatedness using the RELISH corpus -Visit URL Visit ScholarlyArticle +Visit URL Visit Poster - Identifier: DOI:10.4126/FRL01-006440397s +- Cite as: Ravinder R, Fellerhoff T, Dadi VV, Geist L, Rocamora G, Talha M, et al. OntoClue, a framework to compare vector-based approaches for document relatedness using the RELISH corpus - Poster. ZB MED - Informationszentrum Lebenswissenschaften; 2023. Available: https://repository.publisso.de/resource/frl:6440397 - Datepublished: 2023-06-22 +- License: https://spdx.org/licenses/CC-BY-4.0.html +- URL: https://repository.publisso.de/resource/frl:6440397 + +- Authors: https://orcid.org/0009-0004-4484-6283. https://orcid.org/0000-0002-8725-1317. https://orcid.org/0000-0002-3082-7522. https://orcid.org/0000-0002-2910-7982. https://orcid.org/0000-0002-4795-3648. https://zbmed-semtec.github.io/previous_members/#muhammad-talha. https://orcid.org/0000-0002-1018-0370. https://orcid.org/0000-0003-3986-0510. #### OntoClue, a framework to compare vector-based approaches for document relatedness using the RELISH corpus - Poster -Visit URL Visit Poster +Visit URL Visit ScholarlyArticle - Identifier: CEUR:Vol-3415/paper-38 +- Cite as: Ravinder R, Fellerhoff T, Dadi V, Geist L, Rocamora G, Talha M, et al. OntoClue, a framework to compare vector-based approaches for document relatedness using the RELISH corpus. CEUR; 2023. Available: https://ceur-ws.org/Vol-3415/paper-38.pdf - Datepublished: 2023-03-01 +- License: https://spdx.org/licenses/CC-BY-4.0.html +- URL: https://ceur-ws.org/Vol-3415/paper-38.pdf# + +- Authors: https://orcid.org/0009-0004-4484-6283. https://orcid.org/0000-0002-8725-1317. https://orcid.org/0000-0002-3082-7522. https://orcid.org/0000-0002-2910-7982. https://orcid.org/0000-0002-4795-3648. https://zbmed-semtec.github.io/previous_members/#muhammad-talha. https://orcid.org/0000-0002-1018-0370. https://orcid.org/0000-0003-3986-0510. #### Ontology Clustering with OWL2Vec* Visit URL Visit ScholarlyArticle - Identifier: CEUR:Vol-2918/short3 +- Cite as: Ritchie A, Chen J, Castro LJ, Rebholz-Schuhmann D, Jimenez-Ruiz E. Ontology Clustering with OWL2Vec*. CEUR Workshop Proceedings. Online: CEUR Workshop Proceedings; 2021. Available: http://ceur-ws.org/ - Datepublished: 2021-07-28 -#### Creative Commons Attribution 4.0 International - -Visit URL Visit CreativeWork - -- Alternatename: CC BY 4.0 -- URL: https://creativecommons.org/licenses/by/4.0/ +- License: https://spdx.org/licenses/CC-BY-4.0.html +- URL: https://ceur-ws.org/Vol-2918/short3.pdf# +- Authors: https://zbmed-semtec.github.io/previous_members/#ashley-ritchie. https://chenjiaoyan.github.io/. https://orcid.org/0000-0003-3986-0510. https://orcid.org/0000-0002-1018-0370. https://orcid.org/0000-0002-9083-4599. #### Complete Medline abstracts corpus between 2015-2019 annotated Whatizit text annotation tool Visit URL Visit DataCatalog - Identifier: DOI:10.5281/zenodo.5035290 +- Cite as: Lazarov G, Wolff B, Castro LJ, Rebholz-Schuhmann D. Complete Medline abstracts corpus between 2015-2019 annotated Whatizit text annotation tool. Zenodo; 2021. doi:10.5281/zenodo.5035290 - Description: Gene Ontology annotations for Medline abstracts from 2015 to 2019 using Whatizit - Keywords: Whatizit, Semantic annotation, Medline, text-mining -- License: {'@type': 'CreativeWork', '@id': 'https://spdx.org/licenses/CC-BY-4.0.html', 'name': 'Creative Commons Attribution 4.0 International', 'alternateName': 'CC BY 4.0', 'url': 'https://creativecommons.org/licenses/by/4.0/'} +- License: https://spdx.org/licenses/CC-BY-4.0.html - URL: https://zenodo.org/record/5035290 - Datepublished: 2021-06-27 -#### Creative Commons Attribution 4.0 International - -Visit URL Visit CreativeWork - -- Alternatename: CC BY 4.0 -- URL: https://creativecommons.org/licenses/by/4.0/ - +- Authors: https://orcid.org/0000-0002-0762-4305. https://orcid.org/0000-0001-9345-8958. https://orcid.org/0000-0003-3986-0510. https://orcid.org/0000-0002-1018-0370. #### Whatizit performance evaluation against CRAFT corpus Visit URL Visit DataCatalog - Identifier: DOI:10.5281/zenodo.4903981 +- Cite as: Lazarov G, Castro LJ, Rebholz-Schuhmann D. Whatizit performance evaluation against CRAFT corpus. Zenodo; 2021. doi:10.5281/zenodo.4903981 - Description: Whatizit performance evaluation against CRAFT corpus wrt Gene Ontology annotations - Keywords: Whatizit, Semantic annotation, CRAFT, manual annotation, performance -- License: {'@type': 'CreativeWork', '@id': 'https://spdx.org/licenses/CC-BY-4.0.html', 'name': 'Creative Commons Attribution 4.0 International', 'alternateName': 'CC BY 4.0', 'url': 'https://creativecommons.org/licenses/by/4.0/'} +- License: https://spdx.org/licenses/CC-BY-4.0.html - URL: https://zenodo.org/record/4903981 - Datepublished: 2021-06-05 +- Authors: https://orcid.org/0000-0002-0762-4305. https://orcid.org/0000-0003-3986-0510. https://orcid.org/0000-0002-1018-0370. ### External contributors -- Ashley Ritchie Visit URL Visit Person - - Ernesto Jimenez-Ruiz Visit URL Visit Person @@ -152,19 +174,38 @@ word-embeddings, document-embeddings, ontology-embeddings, document similarity, + +## machine-actionable Software Management Plan Ontology (maSMP Ontology) +

Get JSON-LD Get JSON-LD | Visit URL Visit DefinedTermSet

+
+ + + + + + + + + + - + @@ -18,7 +201,7 @@ - + @@ -93,8 +276,16 @@
- - + + + + + + + + + + @@ -111,11 +302,13 @@ { "@context": "https://schema.org/", "@type": "DefinedTermSet", - "@id": "https://doi.org/10.5281/zenodo.8089518", - "name": "maSMP Ontology", + "@id": "https://doi.org/10.5281/zenodo.7806638", + "identifier": "DOI:10.5281/zenodo.7806638", + "citation": "Castro LJ, Giraldo O, Geist L, Qui\u00f1ones N, Solanki D, Rebholz-Schuhmann D. Usage guidance (aka profiles) for the machine-actionable Software Management Plan Ontology. Zenodo; 2024. doi:10.5281/zenodo.10582121", + "name": "machine-actionable Software Management Plan Ontology (maSMP Ontology)", "description": "Metadata model in the form of an ontology representing the necessary metadata elements for a maSMP. The metadata model includes entities involved in software management planning; such as an SMP itself, software source code, software release, documentation, authors and their relations. We are reusing terms mainly from schema.org and from DCSO, with some few additions of our own.", "keywords": "machine-actionability, software management plans, research software, controlled vocabulary, metadata schema", - "archivedAt": "https://zenodo.org/record/8089518", + "archivedAt": "https://doi.org/10.5281/zenodo.7806638", "author": [ { "@type": "Person", @@ -147,7 +340,9 @@ "familyName": "Castro" } ], - "citation": "Giraldo O, Geist L, Qui\u00f1ones N, Solanki D, Rebholz-Schuhmann D, Castro LJ. machine-actionable Software Management Plan Ontology (maSMP Ontology). Zenodo; 2023. doi:10.5281/zenodo.8089518", + "datePublished": "2024-01-29", + "version": "2.1.0", + "url": "https://doi.org/10.5281/zenodo.7806638", "creativeWorkStatus": [ "Published", "In-progress"
identifierDOI:10.5281/zenodo.7806638
citationCastro LJ, Giraldo O, Geist L, Quiñones N, Solanki D, Rebholz-Schuhmann D. Usage guidance (aka profiles) for the machine-actionable Software Management Plan Ontology. Zenodo; 2024. doi:10.5281/zenodo.10582121
namemaSMP Ontologymachine-actionable Software Management Plan Ontology (maSMP Ontology)
description
archivedAthttps://zenodo.org/record/8089518https://doi.org/10.5281/zenodo.7806638
author
citationGiraldo O, Geist L, Quiñones N, Solanki D, Rebholz-Schuhmann D, Castro LJ. machine-actionable Software Management Plan Ontology (maSMP Ontology). Zenodo; 2023. doi:10.5281/zenodo.8089518datePublished2024-01-29
version2.1.0
urlhttps://doi.org/10.5281/zenodo.7806638
creativeWorkStatus