From b8f9e8a24614701f292087f05e6667f94312515a Mon Sep 17 00:00:00 2001
From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com>
Date: Wed, 7 Aug 2024 17:47:56 -0500
Subject: [PATCH] Add mouth rinse specimen term
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src/ontology/modules/biobank-specimens.owl | 150 ++++++++++++++++---
src/ontology/templates/biobank-specimens.tsv | 4 +-
2 files changed, 130 insertions(+), 24 deletions(-)
diff --git a/src/ontology/modules/biobank-specimens.owl b/src/ontology/modules/biobank-specimens.owl
index 01aa098a..bfbb4222 100644
--- a/src/ontology/modules/biobank-specimens.owl
+++ b/src/ontology/modules/biobank-specimens.owl
@@ -22,6 +22,18 @@
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+ A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space.
+ Randi Vita
+ Sebastian Duesing
+ nasal lavage fluid
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- A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space.
- Randi Vita
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+ lavage fluid specimen
+ The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present.
+ A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions.
Sebastian Duesing
- nasal lavage fluid
+ https://github.com/obi-ontology/obi/issues/1803
+ lavage fluid specimen
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+ oral lavage fluid
+ A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space.
+ Sebastian Duesing
+ mouth rinse specimen
+ https://github.com/obi-ontology/obi/issues/1803
+ Anna Maria Masci
+ oral lavage fluid
@@ -3968,6 +4066,12 @@
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diff --git a/src/ontology/templates/biobank-specimens.tsv b/src/ontology/templates/biobank-specimens.tsv
index 7e8c0c84..3bee3d23 100644
--- a/src/ontology/templates/biobank-specimens.tsv
+++ b/src/ontology/templates/biobank-specimens.tsv
@@ -82,7 +82,9 @@ OBI:0003380 placental blood specimen A specimen that is derived from placenta
OBI:0003415 peripheral blood mononuclear cell specimen PBMC specimen A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell Jie Zheng|Chris Stoeckert subclass collecting specimen from organism peripheral blood mononuclear cell CL_2000001
OBI:0003482 lymph specimen A specimen that is derived from a portion of lymph collected from an organism. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 collecting specimen from organism (tissue and ('part of' some lymph)) UBERON_0002391
OBI:0003483 digestive tract specimen A specimen that is derived from part of a digestive tract. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 collecting specimen from organism (tissue and ('part of' some 'digestive tract')) UBERON_0001555
-OBI:0003595 nasal lavage fluid A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. Sebastian Duesing|Randi Vita subclass collecting specimen from organism nasal cavity mucosa UBERON_0001826
+OBI:0003595 nasal lavage fluid A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. Sebastian Duesing|Randi Vita equivalent lavage nasal cavity mucosa UBERON_0001826
+OBI:0003666 lavage fluid specimen lavage fluid specimen A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions. The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1803 equivalent lavage
+OBI:0003667 oral lavage fluid oral lavage fluid mouth rinse specimen A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space. Sebastian Duesing Anna Maria Masci https://github.com/obi-ontology/obi/issues/1803 equivalent lavage mouth UBERON_0000165
OBI:2000000 uterine cervix specimen A specimen that is derived from some uterine cervix Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some 'uterine cervix')) UBERON_0000002
OBI:2000001 urethra specimen A specimen that is derived from some urethra Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some urethra)) UBERON_0000057
OBI:2000002 cervical mucus specimen A specimen that is derived from some cervical mucus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism cervical mucus UBERON_0000316