From a0e030f80ab02ca079ed56f890ee2967659957f5 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Fri, 22 Nov 2024 12:53:39 -0600 Subject: [PATCH] Relabel specified input/output terms to remove underscores --- src/ontology/obi-edit.owl | 20 ++++---- src/ontology/templates/administration.tsv | 2 +- .../templates/antibody-purification.tsv | 2 +- src/ontology/templates/assays.tsv | 6 +-- src/ontology/templates/biopsy.tsv | 2 +- src/ontology/templates/data-sets.tsv | 2 +- .../templates/data-transformations.tsv | 8 +-- src/ontology/templates/devices.tsv | 2 +- src/ontology/templates/epitope-assays.tsv | 2 +- .../templates/physical-examination.tsv | 2 +- src/ontology/templates/sample-collection.tsv | 2 +- src/ontology/templates/sequence-analysis.tsv | 2 +- .../templates/specimen-assay-data.tsv | 50 +++++++++---------- src/ontology/templates/specimens.tsv | 28 +++++------ src/ontology/templates/study-designs.tsv | 2 +- 15 files changed, 66 insertions(+), 66 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 2f30f8bf..a9a30569 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -679,16 +679,16 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - has_specified_input + has specified input see is_input_of example_of_usage - The inverse property of is_specified_input_of + The inverse property of is specified input of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot - has_specified_input + has specified input @@ -714,13 +714,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - is_specified_input_of + is specified input of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - is_specified_input_of + is specified input of @@ -766,14 +766,14 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - has_specified_output + has specified output - The inverse property of is_specified_output_of + The inverse property of is specified output of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot - has_specified_output + has specified output @@ -928,12 +928,12 @@ instance level relation [GOC:cjm] - is_specified_output_of + is specified output of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - is_specified_output_of + is specified output of diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv index aed4b76d..591c8efe 100644 --- a/src/ontology/templates/administration.tsv +++ b/src/ontology/templates/administration.tsv @@ -2,7 +2,7 @@ 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=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and ('role of' some %)) SPLIT=| C 'has part' some % SPLIT=| C achieves_planned_objective some % C % OBI:0000281 intraperitoneal injection intraperitoneal injection is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe BP equivalent intraperitoneal administration ('realizes' some ('function' and ('inheres in' some 'syringe'))) OBI:0000429 intraperitoneal administration intraperitoneal administration The administration of a substance into the peritoneum of an organism Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h Person:Bjoern Peters equivalent administering substance in vivo peritoneum -OBI:0000837 oral ingestion of pill oral ingestion of pill An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case equivalent oral administration pill ('has_specified_input' some 'pill') +OBI:0000837 oral ingestion of pill oral ingestion of pill An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case equivalent oral administration pill ('has specified input' some 'pill') OBI:0000934 intramuscular injection intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe equivalent administering substance in vivo skeletal muscle tissue ('realizes' some ('function' and ('inheres in' some 'syringe'))) OBI:0000942 intradermal injection intradermal injection is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo dermis ('realizes' some ('function' and ('inheres in' some 'syringe'))) OBI:0000952 oral administration oral administration An administering substance in vivo into the mouth of an organism PERSON: Melanie Courtot equivalent administering substance in vivo mouth diff --git a/src/ontology/templates/antibody-purification.tsv b/src/ontology/templates/antibody-purification.tsv index 7227c734..955a911e 100644 --- a/src/ontology/templates/antibody-purification.tsv +++ b/src/ontology/templates/antibody-purification.tsv @@ -1,5 +1,5 @@ id rdfs label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent output -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester SPLIT=| A term tracker item SPLIT=| CLASS_TYPE C % C has_specified_output some % +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester SPLIT=| A term tracker item SPLIT=| CLASS_TYPE C % C 'has specified output' some % OBI:0003616 antibody purification of MHC class I protein complex An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of MHC protein complex MHC class I protein complex OBI:0003617 antibody purification of human MHC class I protein complex An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of MHC class I protein complex human MHC class I protein complex OBI:0003618 antibody purification of HLA protein complex with A2 serotype An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of human MHC class I protein complex HLA protein complex with A2 serotype diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 8e146a7b..3bf66f7c 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class material processing technique detection technique evaluant measurand analyte device reagent molecular label input output target entity target context objective associated axioms -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some % SPLIT=| C 'has part' some ( % and 'detection technique') SPLIT=| C (has_specified_input some (% and 'has role' some 'evaluant role')) and (realizes some ('evaluant role' and ('role of' some %))) SPLIT=| C (has_specified_input some %) and (realizes some ('measurand role' and ('inheres in' some %))) C (has_specified_input some %) and (realizes some ('analyte role' and ('inheres in' some %))) C (has_specified_input some %) and (realizes some (function and ('inheres in' some %))) SPLIT=| C (has_specified_input some %) and (realizes some ('reagent role' and ('inheres in' some %))) C (has_specified_input some %) and (realizes some ('molecular label role' and ('inheres in' some %))) C has_specified_input some % C has_specified_output some % C has_specified_output some ('is about' some %) C has_specified_output some ('is about' some ( 'has assay target context' some %)) C achieves_planned_objective some % C % +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some % SPLIT=| C 'has part' some ( % and 'detection technique') SPLIT=| C ('has specified input' some (% and 'has role' some 'evaluant role')) and (realizes some ('evaluant role' and ('role of' some %))) SPLIT=| C ('has specified input' some %) and (realizes some ('measurand role' and ('inheres in' some %))) C ('has specified input' some %) and (realizes some ('analyte role' and ('inheres in' some %))) C ('has specified input' some %) and (realizes some (function and ('inheres in' some %))) SPLIT=| C ('has specified input' some %) and (realizes some ('reagent role' and ('inheres in' some %))) C ('has specified input' some %) and (realizes some ('molecular label role' and ('inheres in' some %))) C 'has specified input' some % C 'has specified output' some % C 'has specified output' some ('is about' some %) C 'has specified output' some ('is about' some ( 'has assay target context' some %)) C achieves_planned_objective some % C % CHMO:0000087 fluorescence microscopy assay fluorescence imaging|fluorescence microscopic imaging|FM Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores. CHMO subclass light microscopy assay ('material entity' and ('bearer of' some fluorescence)) CHMO:0000089 confocal fluorescence microscopy assay CLSM|confocal fluorescence imaging|confocal laser scanning fluorescence microscopy|confocal laser scanning microscopy|confocal-laser scanning microscopy|fluorescence confocal microscopy|fluorescence confocal scanning laser microscopy|LSCM|scanning confocal fluorescence microscopy Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence. CHMO subclass microscopy assay CHMO:0000102 light microscopy assay light microscopy|OM|optical microscopy Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. CHMO subclass microscopy assay @@ -47,7 +47,7 @@ OBI:0000743 immune response assay metadata incomplete An assay that determines OBI:0000748 bisulfite sequencing assay metadata complete A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. url:https://en.wikipedia.org/wiki/Bisulfite_sequencing PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. Philippe Rocca-Serra|Sagar Jain subclass DNA meth profiling is a epigenetic mod assay, does not need inference DNA methylation profiling assay DNA sequencing assay DNA extract ('deoxyribonucleotide' and ('has part' some 'methyl group')) DNA sequencer DNA extract ('measurement datum' and 'DNA sequence data') epigenetic modification identification objective OBI:0000787 human antithrombin-III in blood assay ready for release AT-III assay An assay that measures the amount of antithrombin III in blood. url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. Alan Ruttenberg subclass analyte assay ('scattered molecular aggregate' and ('has grain' some antithrombin-III)) scalar measurement datum blood coagulation OBI:0000802 prothrombin time assay metadata complete An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). Alan Ruttenberg subclass assay scalar measurement datum blood coagulation -OBI:0000805 antithrombin-III berichrome assay metadata complete AT-III assay An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 subclass human antithrombin-III in blood assay (has_specified_output some 'scalar measurement datum') and ('has participant' some 'Berichrom(r) Antithrombin III (A) Kit') and (has_specified_output exactly 1 Thing) +OBI:0000805 antithrombin-III berichrome assay metadata complete AT-III assay An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 subclass human antithrombin-III in blood assay ('has specified output' some 'scalar measurement datum') and ('has participant' some 'Berichrom(r) Antithrombin III (A) Kit') and ('has specified output' exactly 1 Thing) OBI:0000808 spectrolyse heparin antifactor-Xa assay metadata complete An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration. url:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06 PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland). Alan Ruttenberg subclass assay scalar measurement datum blood coagulation OBI:0000812 measuring neural activity in the caudate nucleus assay metadata complete An assay that measures neural activity in the caudate nucleus Jessica Turner, NIF|Dirk Derom, OBI An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus Helen Parkinson subclass extracellular electrophysiology recording assay OBI:0000820 activated partial thromboplastin time assay metadata complete aPTT assay An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy. url:http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0004310 The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent (PMID:19696660) Alan Ruttenberg|OBI call There is also the 'partial thromboplastin assay', which some people use synonymously to aPPT, but historically was done slightly differently (without adding a coagulant). subclass assay ('blood specimen' or 'blood plasma specimen') time measurement datum blood coagulation @@ -81,7 +81,7 @@ OBI:0000964 in live cell assay metadata incomplete An assay in which a measure OBI:0000966 in live organism assay metadata complete in vivo assay An assay in which a measurement is made by observing entities located in an organism. Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. Bjoern Peters subclass assay ('has participant' some ('material entity' and ('located in' some (organism and ('has quality' some alive))))) OBI:0000975 cell-cell binding detection by flow cytometry assay A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. IEDB Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates. IEDB equivalent cytometry assay flow cytometry assay binding OBI:0000978 in container assay metadata incomplete An assay in which a measurement is made by observing entities located in a container. subclass assay -OBI:0001001 Edinburgh handedness assay metadata complete An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. url:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory|PMID:5146491 Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: ""Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)"" Alan Ruttenberg|Jessica Turner|Gully Burns (orcid:0000-0003-1493-865X) subclass handedness assay Homo sapiens Edinburgh score (has_specified_input value 'Edingburgh handedness inventory') +OBI:0001001 Edinburgh handedness assay metadata complete An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. url:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory|PMID:5146491 Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: ""Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)"" Alan Ruttenberg|Jessica Turner|Gully Burns (orcid:0000-0003-1493-865X) subclass handedness assay Homo sapiens Edinburgh score ('has specified input' value 'Edingburgh handedness inventory') OBI:0001005 RNASE CL3 structure mapping assay ready for release single nucleotide resolution mapping assay using RNAse CL3 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe. RNA ontology PMID:16453415 Philippe Rocca-Serra subclass single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing RNA extract ribonuclease CL3 (chicken) secondary structure of RNA molecule OBI:0001006 CMCT structure mapping assay ready for release single nucleotide resolution mapping assay using CMCT probe A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure RNA ontology PMID:2422386 and PMID:2446263 Philippe Rocca-Serra subclass single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing ('deoxyribonucleic acid' or 'ribonucleic acid') measurement datum secondary structure of sequence macromolecule OBI:0001008 MPE-Fe(II) structure mapping assay ready for release single nucleotide resolution mapping assay using Fe-MP probe A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe. RNA ontology PMID:6209709 Philippe Rocca-Serra subclass single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing RNA extract measurement datum secondary structure of RNA molecule diff --git a/src/ontology/templates/biopsy.tsv b/src/ontology/templates/biopsy.tsv index 3d8e352c..7a4d70c3 100644 --- a/src/ontology/templates/biopsy.tsv +++ b/src/ontology/templates/biopsy.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class material anatomical entity input device output entity -ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE CI C 'has_specified_input' some % C 'has_specified_input' some % C 'has_specified_output' some % +ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE CI C 'has specified input' some % C 'has specified input' some % C 'has specified output' some % OBI:0002650 biopsy ready for release A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. https://en.wikipedia.org/wiki/Biopsy Biopsy of a potentially cancerous mole. Nicole Vasilevsky|Damion Dooley subclass collecting specimen from organism material anatomical entity device pre-mortem specimen OBI:0002651 image guided biopsy ready for release image-guided biopsy|imaging guided biopsy|image guided needle biopsy A biopsy which uses an imaging procedure to guide a needle biopsy. https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland. Damion Dooley subclass needle biopsy OBI:0002652 computed tomography assisted biopsy ready for release Computed Tomography Assisted Biopsy|CT Guided Biopsy|CT Assisted Biopsy|Computed Tomography-Guided Needle Biopsy A needle biopsy guided by real-time computed tomography (CT) scan images. http://purl.obolibrary.org/obo/NCIT_C137909 A CT Guided Biopsy is a procedure performed by a radiologist to obtain a small tissue sample through a needle. Damion Dooley subclass image guided biopsy computed tomography scanner diff --git a/src/ontology/templates/data-sets.tsv b/src/ontology/templates/data-sets.tsv index d1551234..57de9134 100644 --- a/src/ontology/templates/data-sets.tsv +++ b/src/ontology/templates/data-sets.tsv @@ -1,5 +1,5 @@ ontology ID label has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class is about is specified output of has member -ID A rdfs:label AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=, A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE CI C 'is about' some % C is_specified_output_of some % C 'has member' some % +ID A rdfs:label AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=, A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE CI C 'is about' some % C 'is specified output of' some % C 'has member' some % OBI:0003327 image data set A data set that is comprised of multidimensional structured measurements and metadata required for a morphological representation of an entity. An image data set can be the source from which an image (such as a 2D image using pixels or a 3D image using voxels) is produced. The output produced by a digital imaging technique, such as microscopy, MRI, or CT. https://orcid.org/0000-0001-9625-1899 ""William D. Duncan"",https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie"",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/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 subclass data set entity OBI:0003328 magnetic resonance image data set An image data set whose information content originates from some MR imaging assay and is about some MRI participant. MRI at a Glance, ISBN 10: 1119053552 The DICOM file produced by an MRI machine when a multiple sclerosis patient undergoes a brain scan. https://orcid.org/0000-0001-9625-1899 ""William D. Duncan"",https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie"",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/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 equivalent image data set magnetic resonance imaging participant OBI:0003331 raw image data set An image data set that encodes measurement values produced by some instrument before undergoing a data transformation. The untransformed (""k-space"") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. https://orcid.org/0000-0001-9625-1899 ""William D. Duncan"",https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie"",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/0000-0002-9821-4132 ""Mackenzie T. Smith"",https://orcid.org/0000-0002-1604-3078 ""Alan Ruttenberg"" https://github.com/obi-ontology/obi/issues/1481 subclass image data set diff --git a/src/ontology/templates/data-transformations.tsv b/src/ontology/templates/data-transformations.tsv index dbe7caa6..36179101 100644 --- a/src/ontology/templates/data-transformations.tsv +++ b/src/ontology/templates/data-transformations.tsv @@ -1,7 +1,7 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note term tracker item logical type parent class input output objective associated axioms -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en 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 % +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en 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') +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') diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index df3f44ca..fb369a0e 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -309,7 +309,7 @@ OBI:0001204 SNP microarray SNP microarray metadata complete A DNA microarray us OBI:0001307 tiling microarray tiling microarray metadata complete genome tiling array A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. EFO_0002704: tiling array Person: Helen Parkinson DNA microarray OBI:0001865 assay array metadata complete A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg device solid support function OBI:0001869 Illumina BeadChip metadata complete An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. http://www.illumina.com/technology/beadarray_technology.ilmn PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi assay array Illumina -OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina BeadChip ('bearer of' some (function and ('realized in' only (assay and (has_specified_output some ('measurement datum' and ('is about' some (deoxyribonucleotide and ('has part' some 'methyl group'))))))))) +OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina BeadChip ('bearer of' some (function and ('realized in' only (assay and ('has specified output' some ('measurement datum' and ('is about' some (deoxyribonucleotide and ('has part' some 'methyl group'))))))))) OBI:0001871 LSRFortessa X-20 metadata complete A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg Anna Maria Masci flow cytometer analyzer Becton Dickinson (BD Biosciences) OBI:0001971 Ion 316 Chip v2 Ion 316 Chip v2 Ion PGM 316 Chip|Ion 316 Chip|Ion PGM 316 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ ion semiconductor chip OBI:0001972 Ion 318 Chip v2 Ion 318 Chip v2 Ion 318 Chip|Ion PGM 318 Chip|Ion PGM 318 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ ion semiconductor chip diff --git a/src/ontology/templates/epitope-assays.tsv b/src/ontology/templates/epitope-assays.tsv index df7eb494..7e7bc676 100644 --- a/src/ontology/templates/epitope-assays.tsv +++ b/src/ontology/templates/epitope-assays.tsv @@ -1,5 +1,5 @@ Ontology ID label editor preferred term has curation status alternative term IEDB alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class material processing technique detection technique reagent input output MHC source target entity target context unit -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A IEDB alternative term AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some % SPLIT=| C 'has part' some ( % and 'detection technique') SPLIT=| C (has_specified_input some %) and (realizes some ('reagent role' and ('inheres in' some %))) C has_specified_input some % C has_specified_output some % C has_specified_input some (% and ('has part' some 'MHC protein complex')) C has_specified_output some ('is about' some %) C has_specified_output some ('is about' some ( 'has assay target context' some %)) C has_specified_output some ('has measurement unit label' value %) +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A IEDB alternative term AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some % SPLIT=| C 'has part' some ( % and 'detection technique') SPLIT=| C ('has specified input' some %) and (realizes some ('reagent role' and ('inheres in' some %))) C 'has specified input' some % C 'has specified output' some % C 'has specified input' some (% and ('has part' some 'MHC protein complex')) C 'has specified output' some ('is about' some %) C 'has specified output' some ('is about' some ( 'has assay target context' some %)) C 'has specified output' some ('has measurement unit label' value %) OBI:0001194 ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells TGFb release|ELISPOT An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('transforming growth factor beta production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001196 cytometric bead array assay measuring epitope specific IP-10 production by T cells CXCL10/IP-10 release|cytometric bead array A cytometric bead array assay that detects IP-10 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('IP-10 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001198 assay measuring epitope specific interleukin-27 production by T cells IL-27 release|biological activity A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('interleukin-27 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) diff --git a/src/ontology/templates/physical-examination.tsv b/src/ontology/templates/physical-examination.tsv index 7aeb49b3..ea2ebf3f 100644 --- a/src/ontology/templates/physical-examination.tsv +++ b/src/ontology/templates/physical-examination.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class detection technique evaluant device input output anatomical site assessed biological trait -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some ( % and 'detection technique') SPLIT=| C (has_specified_input some (% and 'has role' some 'evaluant role')) and (realizes some ('evaluant role' and ('role of' some %))) SPLIT=| C (has_specified_input some %) and (realizes some (function and ('inheres in' some %))) SPLIT=| C has_specified_input some % C has_specified_output some % C has_specified_output some ('is about' some %) C has_specified_output some ('is quality measurement of' some %) +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some ( % and 'detection technique') SPLIT=| C ('has specified input' some (% and 'has role' some 'evaluant role')) and (realizes some ('evaluant role' and ('role of' some %))) SPLIT=| C ('has specified input' some %) and (realizes some (function and ('inheres in' some %))) SPLIT=| C 'has specified input' some % C 'has specified output' some % C 'has specified output' some ('is about' some %) C 'has specified output' some ('is quality measurement of' some %) OBI:0003501 functional assessment of individual A physical examination of an organism's ability to perform functional activities. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass physical examination of an organism OBI:0003502 facial atrophy assessment An observational assessment of the loss of facial muscle tissue due to inactivity or disease. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass observational assessment of individual facial muscle facial muscle performance OBI:0003503 tongue atrophy assessment An observational assessment of the loss of muscle tissue related to tongue movement due to inactivity or disease. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass observational assessment of individual tongue facial muscle performance diff --git a/src/ontology/templates/sample-collection.tsv b/src/ontology/templates/sample-collection.tsv index c2731ddf..34df2de5 100644 --- a/src/ontology/templates/sample-collection.tsv +++ b/src/ontology/templates/sample-collection.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class specimen type -ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C has_specified_output some (% and 'has role' some 'specimen role') +ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has specified output' some (% and 'has role' some 'specimen role') OBI:0002904 adult arthropod specimen collection process collection of adults A live arthropod specimen collection process in which the arthropods are in the adult stage. MIRO:30000052 John Judkins https://github.com/obi-ontology/obi/issues/1217 live arthropod specimen collection process OBI:0002905 animal-biting arthropod specimen collection by aspiration animal biting catch An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. MIRO:30000012 John Judkins https://github.com/obi-ontology/obi/issues/1217 arthropod specimen collection by aspiration OBI:0002906 animal-biting outdoor arthropod specimen collection by aspiration animal biting catch - outdoors An animal-biting arthropod specimen collection by aspiration that occurs outside a building. MIRO:30000014 John Judkins https://github.com/obi-ontology/obi/issues/1217 animal-biting arthropod specimen collection by aspiration diff --git a/src/ontology/templates/sequence-analysis.tsv b/src/ontology/templates/sequence-analysis.tsv index 9fb69b27..09ce802a 100644 --- a/src/ontology/templates/sequence-analysis.tsv +++ b/src/ontology/templates/sequence-analysis.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class output input input of output of objective -ID A rdfs:label A editor preferred term AL has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has_specified_output' some % C 'has_specified_input' some % C is_specified_input_of some % C is_specified_output_of some % C achieves_planned_objective some % +ID A rdfs:label A editor preferred term AL has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has specified output' some % C 'has specified input' some % C 'is specified input of' some % C 'is specified output of' some % C achieves_planned_objective some % OBI:0002565 adapter-sequence trimming A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). Dan Berrios Dan Berrios subclass sequence trimming adapter-trimmed sequence data 'adapter sequence data' OBI:0002566 file merge A data transformation in which data contained in 2 or more files are merged into a single file. Dan Berrios Dan Berrios subclass data transformation OBI:0002567 sequence alignment A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm. Dan Berrios Dan Berrios subclass sequence analysis data transformation aligned sequence data sequence data diff --git a/src/ontology/templates/specimen-assay-data.tsv b/src/ontology/templates/specimen-assay-data.tsv index 84caaf7d..6bb77a2c 100644 --- a/src/ontology/templates/specimen-assay-data.tsv +++ b/src/ontology/templates/specimen-assay-data.tsv @@ -1,22 +1,22 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item axiom ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item EC % -OBI:0003243 blood assay datum A data item that is the specified output of a blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'blood assay') -OBI:0003244 blood microbiology datum An organism detection datum that is the specified output of a blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'blood microbiology assay') -OBI:0003245 feces assay datum A data item that is the specified output of a feces assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'feces assay') -OBI:0003246 feces microbiology datum An organism detection datum that is the specified output of a feces microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'feces microbiology assay') -OBI:0003247 urine assay datum A data item that is the specified output of a urine assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'urine assay') -OBI:0003248 urine microbiology datum An organism detection datum that is the specified output of a urine microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'urine microbiology assay') -OBI:0003249 induced sputum assay datum A data item that is the specified output of a induced sputum assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'induced sputum assay') -OBI:0003251 induced sputum microbiology datum An organism detection datum that is the specified output of an induced sputum microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'induced sputum microbiology assay') -OBI:0003252 cerebrospinal fluid assay datum A data item that is the specified output of a cerebrospinal fluid assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'cerebrospinal fluid assay') -OBI:0003253 cerebrospinal fluid microbiology datum An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'cerebrospinal fluid microbiology assay') -OBI:0003254 endotracheal aspirate assay datum An organism detection datum that is the specified output of an endotracheal aspirate assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'endotracheal aspirate assay') -OBI:0003255 endotracheal tube aspirate microbiology datum An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'endotracheal tube aspirate microbiology assay') -OBI:0003256 lung microbiology datum An organism detection datum that is the specified output of a lung microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'lung microbiology assay') -OBI:0003257 nasopharyngeal or oropharyngeal swab microbiology datum An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'nasopharyngeal or oropharyngeal swab microbiology assay') -OBI:0003258 pleural fluid microbiology datum An organism detection datum that is the specified output of a pleural fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'pleural fluid microbiology assay') -OBI:0003259 umbilical cord blood assay datum A data item that is the specified output of an umbilical cord blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'umbilical cord blood assay') -OBI:0003260 umbilical cord blood microbiology datum An organism detection datum that is the specified output of an umbilical cord blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'umbilical cord blood microbiology assay') +OBI:0003243 blood assay datum A data item that is the specified output of a blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'blood assay') +OBI:0003244 blood microbiology datum An organism detection datum that is the specified output of a blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'blood microbiology assay') +OBI:0003245 feces assay datum A data item that is the specified output of a feces assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'feces assay') +OBI:0003246 feces microbiology datum An organism detection datum that is the specified output of a feces microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'feces microbiology assay') +OBI:0003247 urine assay datum A data item that is the specified output of a urine assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'urine assay') +OBI:0003248 urine microbiology datum An organism detection datum that is the specified output of a urine microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'urine microbiology assay') +OBI:0003249 induced sputum assay datum A data item that is the specified output of a induced sputum assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'induced sputum assay') +OBI:0003251 induced sputum microbiology datum An organism detection datum that is the specified output of an induced sputum microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'induced sputum microbiology assay') +OBI:0003252 cerebrospinal fluid assay datum A data item that is the specified output of a cerebrospinal fluid assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'cerebrospinal fluid assay') +OBI:0003253 cerebrospinal fluid microbiology datum An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'cerebrospinal fluid microbiology assay') +OBI:0003254 endotracheal aspirate assay datum An organism detection datum that is the specified output of an endotracheal aspirate assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'endotracheal aspirate assay') +OBI:0003255 endotracheal tube aspirate microbiology datum An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'endotracheal tube aspirate microbiology assay') +OBI:0003256 lung microbiology datum An organism detection datum that is the specified output of a lung microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'lung microbiology assay') +OBI:0003257 nasopharyngeal or oropharyngeal swab microbiology datum An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'nasopharyngeal or oropharyngeal swab microbiology assay') +OBI:0003258 pleural fluid microbiology datum An organism detection datum that is the specified output of a pleural fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'pleural fluid microbiology assay') +OBI:0003259 umbilical cord blood assay datum A data item that is the specified output of an umbilical cord blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'umbilical cord blood assay') +OBI:0003260 umbilical cord blood microbiology datum An organism detection datum that is the specified output of an umbilical cord blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'umbilical cord blood microbiology assay') OBI:0003261 bacteria in blood datum A blood microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Bacteria) OBI:0003262 virus in blood datum A blood microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Viruses) OBI:0003263 eukaryota in blood datum A blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Eukaryota) @@ -38,12 +38,12 @@ OBI:0003278 bacteria in pleural fluid datum A pleural fluid microbiology datu OBI:0003279 eukaryota in pleural fluid datum A pleural fluid microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('pleural fluid microbiology datum' and 'is about' some Eukaryota) OBI:0003280 virus in pleural fluid datum A pleural fluid microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('pleural fluid microbiology datum' and 'is about' some Viruses) OBI:0003281 eukaryota in umbilical cord blood datum An umbilical cord blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('umbilical cord blood microbiology datum' and 'is about' some Eukaryota) -OBI:0003365 milk assay datum A data item that is the specified output of a milk assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1515 ('data item' and is_specified_output_of some 'milk assay') -OBI:0003382 placental blood microbiology datum An organism detection datum that is the specified output of a placental blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1297 ('organism detection datum' and is_specified_output_of some 'placental blood microbiology assay') +OBI:0003365 milk assay datum A data item that is the specified output of a milk assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1515 ('data item' and 'is specified output of' some 'milk assay') +OBI:0003382 placental blood microbiology datum An organism detection datum that is the specified output of a placental blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1297 ('organism detection datum' and 'is specified output of' some 'placental blood microbiology assay') OBI:0003383 eukaryota in placental blood datum A placental blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1297 ('placental blood microbiology datum' and 'is about' some Eukaryota) -OBI:0003417 antigen specific antibodies assay datum A data item that is the specified output of an antigen specific antibodies assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('data item' and is_specified_output_of some 'antigen specific antibodies assay') -OBI:0003420 antigen specific antibodies in blood assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and is_specified_output_of some 'blood assay') -OBI:0003421 antigen specific antibodies in milk assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and is_specified_output_of some 'milk assay') -OBI:0003577 skin of body microbiology datum An organism detection datum that is the specified output of a skin of body microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'skin of body microbiology assay') -OBI:0003579 bone marrow microbiology datum An organism detection datum that is the specified output of a bone marrow microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'bone marrow microbiology assay') -OBI:0003581 nasal aspirate microbiology datum An organism detection datum that is the specified output of a nasal aspirate microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'nasal aspirate microbiology assay') +OBI:0003417 antigen specific antibodies assay datum A data item that is the specified output of an antigen specific antibodies assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('data item' and 'is specified output of' some 'antigen specific antibodies assay') +OBI:0003420 antigen specific antibodies in blood assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and 'is specified output of' some 'blood assay') +OBI:0003421 antigen specific antibodies in milk assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and 'is specified output of' some 'milk assay') +OBI:0003577 skin of body microbiology datum An organism detection datum that is the specified output of a skin of body microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and 'is specified output of' some 'skin of body microbiology assay') +OBI:0003579 bone marrow microbiology datum An organism detection datum that is the specified output of a bone marrow microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and 'is specified output of' some 'bone marrow microbiology assay') +OBI:0003581 nasal aspirate microbiology datum An organism detection datum that is the specified output of a nasal aspirate microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and 'is specified output of' some 'nasal aspirate microbiology assay') diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index 28cc0148..934e7a7d 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class specimen collection process gross anatomical part collection process input associated axioms URI -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C is_specified_output_of some % C (is_specified_output_of some 'specimen collection process') and ('derives from' some %) C is_specified_output_of some ('specimen collection process' and has_specified_input some %) C % SPLIT=| +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'is specified output of' some % C ('is specified output of' some 'specimen collection process') and ('derives from' some %) C 'is specified output of' some ('specimen collection process' and 'has specified input' some %) C % SPLIT=| OBI:0000651 urine specimen urine specimen metadata complete a portion of urine collected from an organism This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active|are we happy calling collection of urine a material separation?|4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. equivalent specimen from organism collecting specimen from organism urine OBI:0000655 blood specimen blood specimen ready for release a material entity derived from a portion of blood collected from an organism Bjoern Peters blood drawn from a human for glucose assay Bjoern Peters equivalent specimen from organism collecting specimen from organism blood OBI:0000671 sample from organism sample from organism example to be eventually removed a material obtained from an organism in order to be a representative of the whole we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.|5/29: This is a helper class for now equivalent specimen from organism 'has role' some 'material sample role' @@ -14,23 +14,23 @@ OBI:0000880 RNA extract RNA extract metadata complete an extract which is the o OBI:0000895 total RNA extract total RNA extract metadata complete A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. UPenn Group Extraction of total RNA from cells with Qiagen mini RNeasy kit PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass RNA extract total RNA extraction OBI:0000899 organellar RNA extract organellar RNA extract metadata complete A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. UPenn Group Extraction of organellar RNA from plant cells using organellar RNA binding protein. PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass RNA extract organellar RNA extraction OBI:0000902 post mortem specimen post mortem specimen metadata complete a specimen that was taken from a dead organism MO_416 postmortem the spleen taken from a dead mouse Bjoern Peters equivalent specimen with pre- or post-mortem status ('organism' and ('has quality' some 'dead')) -OBI:0000908 labeled DNA extract labeled DNA extract metadata complete a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call equivalent labeled nucleic acid extract ('addition of molecular label' and ('has_specified_input' some 'DNA extract')) 'has grain' some 'deoxyribonucleic acid' +OBI:0000908 labeled DNA extract labeled DNA extract metadata complete a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call equivalent labeled nucleic acid extract ('addition of molecular label' and ('has specified input' some 'DNA extract')) 'has grain' some 'deoxyribonucleic acid' OBI:0000909 cloacal specimen cell specimen metadata complete A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot equivalent specimen from organism collecting specimen from organism cloaca OBI:0000914 nasopharyngeal aspirate specimen nasopharyngeal aspirate specimen metadata complete A specimen which derives from nasopharyngeal mucosa after aspiration. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot subclass specimen from organism collecting specimen from organism nasopharynx OBI:0000917 nasal swab specimen nasal swab specimen metadata complete A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot equivalent specimen from organism collecting specimen with swab nasal cavity mucosa -OBI:0000921 labeled RNA extract labeled RNA extract metadata complete a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call equivalent labeled nucleic acid extract ('addition of molecular label' and ('has_specified_input' some 'RNA extract')) 'has grain' some 'ribonucleic acid' -OBI:0000922 frozen specimen frozen specimen metadata incomplete A specimen that has been frozen in order to store it. MO_610 frozen_sample Frozen blood plasma Person:Alan Ruttenberg equivalent specimen ('freezing storage' and ('has_specified_input' some ('has role' some 'specimen role'))) +OBI:0000921 labeled RNA extract labeled RNA extract metadata complete a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call equivalent labeled nucleic acid extract ('addition of molecular label' and ('has specified input' some 'RNA extract')) 'has grain' some 'ribonucleic acid' +OBI:0000922 frozen specimen frozen specimen metadata incomplete A specimen that has been frozen in order to store it. MO_610 frozen_sample Frozen blood plasma Person:Alan Ruttenberg equivalent specimen ('freezing storage' and ('has specified input' some ('has role' some 'specimen role'))) OBI:0000924 labeled specimen labeled specimen metadata incomplete A specimen that has been modified in order to be able to detect it in future experiments OBI group added during call 3/1/2010 equivalent specimen addition of molecular label 'has part' some 'molecular label' -OBI:0000950 paraffin specimen paraffin specimen metadata incomplete a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin MO_990 paraffin_sample liver tissue embedded in paraffin PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('paraffin storage' and ('has_specified_input' some ('has role' some 'specimen role'))) +OBI:0000950 paraffin specimen paraffin specimen metadata incomplete a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin MO_990 paraffin_sample liver tissue embedded in paraffin PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('paraffin storage' and ('has specified input' some ('has role' some 'specimen role'))) OBI:0000953 processed specimen processed specimen ready for release A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. equivalent specimen 'processed material' and 'specimen' -OBI:0000965 lyophilized specimen lyophilized specimen metadata incomplete a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. MO_589 freeze_dried_sample freezing dried DNA PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('lyophilization storage' and ('has_specified_input' some ('has role' some 'specimen role'))) +OBI:0000965 lyophilized specimen lyophilized specimen metadata incomplete a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. MO_589 freeze_dried_sample freezing dried DNA PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('lyophilization storage' and ('has specified input' some ('has role' some 'specimen role'))) OBI:0000971 fresh specimen fresh specimen metadata incomplete a specimen that is output of a specimen creation process used for an investigation without storage. MO_730 fresh_sample a liver freshly removed from a rat PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass specimen with known storage state -OBI:0000981 agar stab specimen agar stab specimen metadata incomplete a specimen that is output of a process that cell culture inoculated into agar for long term storage. MO_971 agar_stab PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('agar stab storage' and ('has_specified_input' some ('has role' some 'specimen role'))) +OBI:0000981 agar stab specimen agar stab specimen metadata incomplete a specimen that is output of a process that cell culture inoculated into agar for long term storage. MO_971 agar_stab PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('agar stab storage' and ('has specified input' some ('has role' some 'specimen role'))) OBI:0001010 nucleic acid extract nucleic acid extract metadata complete An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. UPenn Group Person: Jie Zheng subclass specimen nucleic acid extraction OBI:0001051 DNA extract DNA extract metadata complete The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Group: UPenn group Person: Jie Zheng subclass nucleic acid extract DNA extraction 'has grain' some 'deoxyribonucleic acid' -OBI:0001143 labeled nucleic acid extract labeled nucleic acid extract metadata complete labeled extract a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. MO_221 labeledExtract Person: Jie Zheng equivalent labeled specimen ('addition of molecular label' and ('has_specified_input' some 'nucleic acid extract')) 'has grain' some 'nucleic acid' +OBI:0001143 labeled nucleic acid extract labeled nucleic acid extract metadata complete labeled extract a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. MO_221 labeledExtract Person: Jie Zheng equivalent labeled specimen ('addition of molecular label' and ('has specified input' some 'nucleic acid extract')) 'has grain' some 'nucleic acid' OBI:0001468 cell specimen cell specimen metadata incomplete A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. MO_612 cell PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828 equivalent specimen from organism 'has part' some 'cell' -OBI:0001472 specimen with known storage state specimen with known storage state metadata incomplete A specimen for which it is known whether it has been subjected to storage of a specified type. MO_95 BiosourceType PERSON: Chris Stoeckert, Jie Zheng equivalent specimen 'fresh specimen' or ('specimen' and ('is_specified_output_of' some 'storage')) +OBI:0001472 specimen with known storage state specimen with known storage state metadata incomplete A specimen for which it is known whether it has been subjected to storage of a specified type. MO_95 BiosourceType PERSON: Chris Stoeckert, Jie Zheng equivalent specimen 'fresh specimen' or ('specimen' and ('is specified output of' some 'storage')) OBI:0001479 specimen from organism ready for release tissue specimen A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). MO_954 organism_part PERSON: Chris Stoeckert, Jie Zheng equivalent specimen ('organism' or 'material anatomical entity' or 'anatomical cluster') OBI:0001506 specimen with pre- or post-mortem status specimen with pre- or post-mortem status metadata complete A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. MO_84 OrganismStatus PERSON: Chris Stoeckert, Jie Zheng organizational term, used in description of specimen that is created from known pre- or post-mortem status equivalent specimen ('organism' and ('has quality' some ('alive' or 'dead'))) OBI:0002125 H&E-stained fixed tissue slide specimen H&E-stained fixed tissue slide specimen pending final vetting A fixed tissue slide specimen that is the output of H&E slide staining. OBIB, OBI Chris Stoeckert, Ned Haubein equivalent fixed tissue slide specimen H&E slide staining @@ -128,13 +128,13 @@ OBI:0003595 nasal lavage fluid A specimen collected through nasal cavity lava OBI:0003652 albumin-free serum albumin-free serum A blood serum specimen that contains no albumin. Sebastian Duesing Philippe Rocca-Serra https://github.com/obi-ontology/obi/issues/493 equivalent blood serum specimen 'has part' only (not ('albumin')) 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 specimen from organism 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 fluid specimen lavage mouth UBERON_0000165 -OBI:0100016 blood plasma specimen blood plasma specimen metadata complete plasma a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. WEB: http://en.wikipedia.org/wiki/Blood_plasma PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. PERSON: Maura Gasparetto|PERSON: Melanie Courtot|PERSON: Philippe Rocca-Serra 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. subclass blood specimen ('material component separation' and ('has_specified_input' some 'blood specimen')) -OBI:0100017 blood serum specimen blood serum specimen metadata complete A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. WEB: http://en.wikipedia.org/wiki/Blood_plasma PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. PERSON: Maura Gasparetto|PERSON: Melanie Courtot|PERSON: Philippe Rocca-Serra subclass blood plasma specimen (('filtration' or 'centrifugation' or 'dialysis') and ('has_specified_input' some 'blood specimen')) +OBI:0100016 blood plasma specimen blood plasma specimen metadata complete plasma a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. WEB: http://en.wikipedia.org/wiki/Blood_plasma PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. PERSON: Maura Gasparetto|PERSON: Melanie Courtot|PERSON: Philippe Rocca-Serra 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. subclass blood specimen ('material component separation' and ('has specified input' some 'blood specimen')) +OBI:0100017 blood serum specimen blood serum specimen metadata complete A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. WEB: http://en.wikipedia.org/wiki/Blood_plasma PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. PERSON: Maura Gasparetto|PERSON: Melanie Courtot|PERSON: Philippe Rocca-Serra subclass blood plasma specimen (('filtration' or 'centrifugation' or 'dialysis') and ('has specified input' some 'blood specimen')) OBI:0100067 bronchial alveolar lavage bronchial alveolar lavage metadata complete BAL Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. GROUP: IEDB solution containing lung derived T cells, eosinophils, and TNFa. PERSON: Bjoern Peters equivalent lavage fluid specimen lavage lung -OBI:0302716 pool of specimens pool of specimens metadata complete A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. GROUP: CEBS PERSON: Jennifer Fostel check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish equivalent specimen ('material combination' and ('has_specified_input' only 'specimen')) +OBI:0302716 pool of specimens pool of specimens metadata complete A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. GROUP: CEBS PERSON: Jennifer Fostel check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish equivalent specimen ('material combination' and ('has specified input' only 'specimen')) OBI:1000049 whole mount tissue whole mount tissue metadata complete whole mount sample A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide GROUP: OBI PERSON: Helen Parkinson|PERSON: Philippe Rocca-Serra PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity|PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application subclass whole organism preparation histological sample preparation 'derives from' some 'material anatomical entity' -OBI:1110041 lymph node cell specimen lymph node cell specimen metadata incomplete A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB equivalent cell specimen ('organ harvesting' and ('has_specified_input' some 'lymph node')) -OBI:1110116 splenocyte specimen splenocyte specimen metadata complete A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB equivalent cell specimen ('organ harvesting' and ('has_specified_input' some 'spleen')) +OBI:1110041 lymph node cell specimen lymph node cell specimen metadata incomplete A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB equivalent cell specimen ('organ harvesting' and ('has specified input' some 'lymph node')) +OBI:1110116 splenocyte specimen splenocyte specimen metadata complete A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB equivalent cell specimen ('organ harvesting' and ('has specified input' some 'spleen')) OBI:1200000 FFPE specimen FFPE specimen formalin-fixed paraffin-embeded specimen A specimen that has been fixed in formalin and embedded in paraffin. https://www.biochain.com/general/what-is-ffpe-tissue/ Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/ MIABIS https://github.com/obi-ontology/obi/issues/1019 subclass paraffin specimen 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 specimen from organism 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 specimen from organism collecting specimen from organism (tissue and ('part of' some urethra)) UBERON_0000057 diff --git a/src/ontology/templates/study-designs.tsv b/src/ontology/templates/study-designs.tsv index 50ae1a83..a3a15ad3 100644 --- a/src/ontology/templates/study-designs.tsv +++ b/src/ontology/templates/study-designs.tsv @@ -34,7 +34,7 @@ OBI:0001337 clinical history design clinical history design metadata complete A OBI:0001358 post-transcriptional modification design post-transcriptional modification design metadata complete A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. MO_392 cellular_modification_design Person: Chris Stoeckert, Jie Zheng post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases subclass intervention design biological feature identification objective study intervention OBI:0001365 cellular process design cellular process design metadata complete A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. MO_810 cellular_process_design Person: Chris Stoeckert, Jie Zheng subclass study design ('cellular feature identification objective' and ('is about' some 'cellular process')) OBI:0001374 injury design injury design metadata complete A study design in which the response of an organism(s) to injury or damage is studied. MO_726 injury_design Person: Chris Stoeckert, Jie Zheng subclass study design organism feature identification objective -OBI:0001377 organism status comparison design organism status comparison design metadata complete A study design that compares samples from live and dead organisms. MO_841 organism_status_design Person: Chris Stoeckert, Jie Zheng subclass study design biological feature identification objective ('is concretized as' some ('realized in' some (assay and (has_specified_input some ('pre-mortem specimen' or 'post mortem specimen'))))) +OBI:0001377 organism status comparison design organism status comparison design metadata complete A study design that compares samples from live and dead organisms. MO_841 organism_status_design Person: Chris Stoeckert, Jie Zheng subclass study design biological feature identification objective ('is concretized as' some ('realized in' some (assay and ('has specified input' some ('pre-mortem specimen' or 'post mortem specimen'))))) OBI:0001387 genotyping by array design genotyping by array design metadata complete A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. MO_560 genotyping_design Person: Chris Stoeckert, Jie Zheng subclass genotyping design OBI:0001396 stimulus or stress design stimulus or stress design metadata complete A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. MO_568 stimulus_or_stress_design Person: Chris Stoeckert, Jie Zheng subclass intervention design ('organism feature identification objective' and ('is about' some 'response to stimulus')) study intervention OBI:0001401 protocol optimization design protocol optimization design metadata complete A study design where different protocols or protocol parameters are compared aims to find an optimized protocol MO_934 optimization_design Person: Chris Stoeckert, Jie Zheng subclass study design protocol optimization objective