From 321624bff2b63ef76fbc62d455e968eeb60a86bc Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 9 Nov 2023 12:43:15 -0600 Subject: [PATCH 1/8] Add mass spectrometry analysis terms --- src/ontology/modules/data-transformations.owl | 173 ++++++++++++++++-- .../templates/data-transformations.tsv | 3 + 2 files changed, 163 insertions(+), 13 deletions(-) diff --git a/src/ontology/modules/data-transformations.owl b/src/ontology/modules/data-transformations.owl index 110a5ba4..682dd8da 100644 --- a/src/ontology/modules/data-transformations.owl +++ b/src/ontology/modules/data-transformations.owl @@ -22,6 +22,12 @@ + + + + + + @@ -40,6 +46,12 @@ + + + + + + @@ -69,6 +81,12 @@ + + + + + + + + + + + + + + + + + + + + + + + @@ -109,12 +145,12 @@ The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 image data set analysis @@ -139,23 +175,134 @@ - A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined. + A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined. A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 raw magnetic resonance image data set reconstruction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tandem mass spectrometry analysis + Sebastian Duesing + A mass spectrometry analysis in which the data being analyzed is the result of a tandem mass spectrometry assay. + https://github.com/obi-ontology/obi/issues/1684 + tandem mass spectrometry analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + liquid chromatography mass spectrometry analysis + Sebastian Duesing + A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography mass spectrometry assay. + https://github.com/obi-ontology/obi/issues/1684 + liquid chromatrography mass spectrometry analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + liquid chromatography tandem mass spectrometry analysis + Sebastian Duesing + A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography tandem mass spectrometry assay. + https://github.com/obi-ontology/obi/issues/1684 + liquid chromatography-tandem mass spectrometry analysis + + + + + + + + + + diff --git a/src/ontology/templates/data-transformations.tsv b/src/ontology/templates/data-transformations.tsv index 3a3d1c03..69694ebf 100644 --- a/src/ontology/templates/data-transformations.tsv +++ b/src/ontology/templates/data-transformations.tsv @@ -2,3 +2,6 @@ ontology ID label editor preferred term has curation status alternative term def ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A term tracker item CLASS_TYPE C % C has_specified_input some % C has_specified_output some % C achieves_planned_objective some % C % OBI:0003355 image data set analysis The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item. https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik""|https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl""|https://orcid.org/0000-0001-9625-1899 ""William D. Duncan""|https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra""|https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie""|https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 subclass data transformation image data set OBI:0003356 raw magnetic resonance image data set reconstruction A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. A Fourier transform of raw ""k-space"" data produced into an image data set that represents the anatomical structure of the tissue examined. https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik""|https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl""|https://orcid.org/0000-0001-9625-1899 ""William D. Duncan""|https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra""|https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie""|https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 equivalent image data set analysis raw magnetic resonance image data set reconstructed magnetic resonance image data set +OBI:0003647 tandem mass spectrometry analysis tandem mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a tandem mass spectrometry assay. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1684 equivalent mass spectrometry analysis ('data item' and is_specified_output_of some 'tandem mass spectrometry assay') +OBI:0003648 liquid chromatrography mass spectrometry analysis liquid chromatography mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography mass spectrometry assay. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1684 equivalent mass spectrometry analysis ('data item' and is_specified_output_of some 'liquid chromatography mass spectrometry assay') +OBI:0003649 liquid chromatography-tandem mass spectrometry analysis liquid chromatography tandem mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography tandem mass spectrometry assay. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1684 equivalent mass spectrometry analysis ('data item' and is_specified_output_of some 'liquid chromatography-tandem mass spectrometry') From 94268e5618c84ea805d283eefa96bd20507c8500 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 16 Nov 2023 12:24:36 -0600 Subject: [PATCH 2/8] Removing check on definition comments --- src/ontology/modules/devices.owl | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl index b5b64c16..d3fdb7fb 100644 --- a/src/ontology/modules/devices.owl +++ b/src/ontology/modules/devices.owl @@ -1043,7 +1043,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 - check on definition ! solvent mixer @@ -1964,7 +1963,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 - chromatography device, check on definition ! column cartridge @@ -2192,7 +2190,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 - check on definition ! column cartridger @@ -2223,7 +2220,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065 - chromatography device, check on definition ! needle assembly From a6be2f7a7bbb1e831dff45159a7ae52ce053fea1 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 16 Nov 2023 12:31:07 -0600 Subject: [PATCH 3/8] Update illumina methylationEPIC v1.0 & v2.0 beadchips --- src/ontology/modules/devices.owl | 22 ++++++++++++++++------ src/ontology/templates/devices.tsv | 3 ++- 2 files changed, 18 insertions(+), 7 deletions(-) diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl index b5b64c16..4e31ff82 100644 --- a/src/ontology/modules/devices.owl +++ b/src/ontology/modules/devices.owl @@ -1043,7 +1043,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 - check on definition ! solvent mixer @@ -1964,7 +1963,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 - chromatography device, check on definition ! column cartridge @@ -2192,7 +2190,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 - check on definition ! column cartridger @@ -2223,7 +2220,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065 - chromatography device, check on definition ! needle assembly @@ -6949,12 +6945,12 @@ - Illumina Infinium MethylationEPIC BeadChip + Illumina Infinium MethylationEPIC v1.0 BeadChip An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. Person: Chris Stoeckert, Jason Hilton http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf - Illumina Infinium MethylationEPIC BeadChip + Illumina Infinium MethylationEPIC v1.0 BeadChip @@ -9136,6 +9132,20 @@ + + + + + Illumina Infinium MethylationEPIC v2.0 BeadChip + An Illumina methylation BeadChip that targets 935,000 methylation sites per sample at single-nucleotide resolution. + Sebastian Duesing + https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html + https://github.com/obi-ontology/obi/issues/1665 + Illumina Infinium MethylationEPIC v2.0 BeadChip + + + + diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index 4443e87b..9e1b4426 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -345,7 +345,7 @@ OBI:0002109 Human 6x630K CGH Whole Genome Tiling Array ready for release Nimble OBI:0002128 Illumina Genome Analyzer Illumina Genome Analyzer pending final vetting Illumina Genome Analyzer I A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html Person: Chris Stoeckert, Jason Hilton DNA sequencer OBI:0002129 Illumina HiSeq X Ten Illumina HiSeq X Ten pending final vetting HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann DNA sequencer OBI:0002130 Illumina Infinium Omni5Exome-4 Kit Illumina Infinium Omni5Exome-4 Kit pending final vetting An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html Person: Chris Stoeckert, Jason Hilton Illumina BeadChip -OBI:0002131 Illumina Infinium MethylationEPIC BeadChip Illumina Infinium MethylationEPIC BeadChip pending final vetting An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf Person: Chris Stoeckert, Jason Hilton Illumina methylation BeadChip +OBI:0002131 Illumina Infinium MethylationEPIC v1.0 BeadChip Illumina Infinium MethylationEPIC v1.0 BeadChip pending final vetting An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf Person: Chris Stoeckert, Jason Hilton Illumina methylation BeadChip OBI:0002192 Leica Peloris rapid tissue processor Leica Peloris rapid tissue processor ready for release An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories. http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf Chris Stoeckert, Helena Ellis NCI BBRB automatic tissue processor OBI:0002194 Microm Ergostar HM200 Microm Ergostar HM200 ready for release A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right. http://www.ultra-medical.com/Microm-Ergostar-HM200-Microtome/en Chris Stoeckert, Helena Ellis NCI BBRB microtome OBI:0002195 microtome blade microtome blade ready for release A device that is the part of a microtome used to slice specimens to a desired thickness. https://en.wikipedia.org/wiki/Microtome Chris Stoeckert, Helena Ellis NCI BBRB device @@ -468,6 +468,7 @@ OBI:0003494 Advantage Chikungunya IgM Card kit An assay kit that is manufactu OBI:0003550 odor baited CDC light trap human odour baited light trap A CDC light trap that uses odorous gas from a human being as an attractant, by pumping it from the room where the human being sleeps into the trap. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1654 Centers for Disease Control and Prevention light trap OBI:0003551 resting clay pot trap resting clay pot catch A resting arthropod trap that consists of a container composed primarily of clay. John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1651 resting arthropod trap OBI:0003606 Illumina NextSeq 1000 NextSeq 1000 A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html Sebastian Duesing GENEPIO https://github.com/obi-ontology/obi/issues/1711 subclass DNA sequencer Illumina +OBI:0003650 Illumina Infinium MethylationEPIC v2.0 BeadChip Illumina Infinium MethylationEPIC v2.0 BeadChip An Illumina methylation BeadChip that targets 935,000 methylation sites per sample at single-nucleotide resolution. https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html Sebastian Duesing https://github.com/obi-ontology/obi/issues/1665 Illumina methylation BeadChip OBI:0400005 A10-Analyzer A10-Analyzer ready for release A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer OBI:0400006 A40-MiniFCM A40-MiniFCM ready for release A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer OBI:0400007 analog-to-digital converter analog-to-digital converter metadata incomplete A2D|A-D An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. http://en.wiktionary.org/wiki/Analog-to-Digital_Converter The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. John Quinn|Melanie Courtot device signal conversion function From e71ad68ac145471d0d5cff82972b5d576103ebeb Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Tue, 21 Nov 2023 12:00:27 -0600 Subject: [PATCH 4/8] Update due to change in OWL API quotation mark handling --- src/ontology/modules/data-transformations.owl | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/src/ontology/modules/data-transformations.owl b/src/ontology/modules/data-transformations.owl index 110a5ba4..fb8b9c36 100644 --- a/src/ontology/modules/data-transformations.owl +++ b/src/ontology/modules/data-transformations.owl @@ -109,12 +109,12 @@ The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 image data set analysis @@ -139,14 +139,14 @@ - A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined. + A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined. A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 raw magnetic resonance image data set reconstruction From b6dca8fae7ae66fd826632886911a6aa50c8d1e0 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Tue, 28 Nov 2023 14:07:22 -0600 Subject: [PATCH 5/8] Obsoleting OBI's CD8 receptor class in favor of PR term --- src/ontology/modules/obsolete.owl | 20 ++++++++++++++++++++ src/ontology/obi-edit.owl | 3 +-- src/ontology/templates/obsolete.tsv | 1 + 3 files changed, 22 insertions(+), 2 deletions(-) diff --git a/src/ontology/modules/obsolete.owl b/src/ontology/modules/obsolete.owl index a9d381f0..d1a15197 100644 --- a/src/ontology/modules/obsolete.owl +++ b/src/ontology/modules/obsolete.owl @@ -76,6 +76,12 @@ + + + + + + @@ -1140,6 +1146,20 @@ + + + + + A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. + CD8 + https://github.com/obi-ontology/obi/issues/353 + + obsolete CD8 receptor + true + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 509f0623..6b70d264 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -31871,7 +31871,6 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - CD8 receptor A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. @@ -33496,5 +33495,5 @@ realizes some 'host of immune response role' - + diff --git a/src/ontology/templates/obsolete.tsv b/src/ontology/templates/obsolete.tsv index 200ddb54..3cb52b68 100755 --- a/src/ontology/templates/obsolete.tsv +++ b/src/ontology/templates/obsolete.tsv @@ -67,5 +67,6 @@ OBI:0600003 obsolete performing a clinical assessment metadata complete clinica OBI:0600065 obsolete_defined processes organizational term Place holder class, see editor note OBI branch derived PlanAndPlannedProcess Branch subclass Obsolete Class true IAO:0000226 OBI:1110002 obsolete_occurrence of disease metadata incomplete An occurrence of disease is a process involving pathologic changes within an organism IEDB IEDB subclass Obsolete Class true IAO:0000228 OBI:1110055 obsolete_disease organizational term placeholder to be imported from disease ontology IEDB IEDB subclass Obsolete Class true IAO:0000228 OGMS:0000031 +OBI:1110132 obsolete CD8 receptor CD8 A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. https://github.com/obi-ontology/obi/issues/353 subclass Obsolete Class true PR:000025402 REO:0000171 obsolete molecular label role ready for release molecular tracer role A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. OBI developer call, 3-12-12 Group: OBI subclass Obsolete Class true OBI:0002743 REO:0000280 obsolete molecular label ready for release molecular tracer A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay OBI developer call, 3-12-12 Group: OBI subclass Obsolete Class true OBI:0002744 From 6cb80b1323ec6b3cf27d178f73f965252ccc4d00 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Tue, 28 Nov 2023 15:39:20 -0600 Subject: [PATCH 6/8] Adds MFI score term for HCC --- src/ontology/obi-edit.owl | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 509f0623..c9a48eb8 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -22422,6 +22422,18 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + A clinical data item that quantifies the severity of a person's fatigue as measured by a 20-item self-report instrument. + Sebastian Duesing + https://pubmed.ncbi.nlm.nih.gov/7636775/ DOI: 10.1016/0022-3999(94)00125-o + multidimensional fatigue inventory score + + + + @@ -33496,5 +33508,5 @@ realizes some 'host of immune response role' - + From 05330c02c5f3e81082b461b6cce6e6ebe0f32886 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 30 Nov 2023 12:16:40 -0600 Subject: [PATCH 7/8] removing cd8 receptor obsoleted term from obi-edit --- src/ontology/obi-edit.owl | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 6b70d264..5ada1e03 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -31868,20 +31868,6 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - - CD8 receptor - - A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. - This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009. - CD8 - WEB: http://en.wikipedia.org/wiki/CD8 - CD8 receptor - - - - From 524212a43137263858404afd5ec8f7c50617553f Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 30 Nov 2023 12:21:38 -0600 Subject: [PATCH 8/8] removing uses of cd8 receptor obsolete term --- src/ontology/obi-edit.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 5ada1e03..aac49a88 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -31134,7 +31134,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -31173,7 +31173,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -31181,7 +31181,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - +