From b4e829d54fa4c67526c0de45d29843b09dd006fe Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 27 Nov 2024 20:26:46 +0100 Subject: [PATCH 1/9] Add missing taxranks that appear in NCBI Taxonomy Database Closes #4 --- src/ontology/taxrank-edit.obo | 94 +++++++++++++++++++++++++++++++++++ 1 file changed, 94 insertions(+) diff --git a/src/ontology/taxrank-edit.obo b/src/ontology/taxrank-edit.obo index 24d2e9a..146df9c 100644 --- a/src/ontology/taxrank-edit.obo +++ b/src/ontology/taxrank-edit.obo @@ -446,6 +446,100 @@ def: "A token asserting that the taxon was not assigned a rank." [TAXRANK:curato is_a: TAXRANK:0000000 ! taxonomic_rank created_by: pmidford + +[Term] +id: TAXRANK:0001001 +name: strain +xref: NCBITaxon:strain +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Azotobacter chroococcum (strain mcd 1) (NCBITaxon:355) is a strain" +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001002 +name: isolate +xref: NCBITaxon:isolate +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Plasmodium falciparum FCR-3/Gambia (NCBITaxon:5838) is an isolate" +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001003 +name: serotype +xref: NCBITaxon:serotype +is_a: TAXRANK:0000000 ! taxonomic_rank +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001004 +name: clade +xref: NCBITaxon:clade +is_a: TAXRANK:0000000 ! taxonomic_rank +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001005 +name: forma specialis +xref: NCBITaxon:forma_specialis +is_a: TAXRANK:0000000 ! taxonomic_rank +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001006 +name: serogroup +xref: NCBITaxon:serogroup +is_a: TAXRANK:0000000 ! taxonomic_rank +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001007 +name: genotype +xref: NCBITaxon: genotype +is_a: TAXRANK:0000000 ! taxonomic_rank +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001008 +name: biotype +xref: NCBITaxon: biotype +is_a: TAXRANK:0000000 ! taxonomic_rank +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001009 +name: morph +xref: NCBITaxon:morph +is_a: TAXRANK:0000000 ! taxonomic_rank +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001010 +name: cohort +xref: NCBITaxon:cohort +is_a: TAXRANK:0000000 ! taxonomic_rank +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001011 +name: pathogroup +xref: NCBITaxon:pathogroup +is_a: TAXRANK:0000000 ! taxonomic_rank +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001012 +name: subcohort +xref: NCBITaxon:subcohort +is_a: TAXRANK:0000000 ! taxonomic_rank +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + +[Term] +id: TAXRANK:0001013 +name: +xref: NCBITaxon: +is_a: TAXRANK:0000000 ! taxonomic_rank +created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt + [Typedef] id: TAXRANK:1000000 name: has_rank From e5cbcf6c6a142446722d59c142cf4d4256b703ae Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 27 Nov 2024 20:34:17 +0100 Subject: [PATCH 2/9] Add examples --- src/ontology/taxrank-edit.obo | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/ontology/taxrank-edit.obo b/src/ontology/taxrank-edit.obo index 146df9c..fb4c8a7 100644 --- a/src/ontology/taxrank-edit.obo +++ b/src/ontology/taxrank-edit.obo @@ -468,6 +468,7 @@ id: TAXRANK:0001003 name: serotype xref: NCBITaxon:serotype is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Bovine adenovirus 3 (NCBITaxon:10510) is a serotype" created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -475,6 +476,7 @@ id: TAXRANK:0001004 name: clade xref: NCBITaxon:clade is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Embryophyta (NCBITaxon:3193) is a clade" created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -482,6 +484,7 @@ id: TAXRANK:0001005 name: forma specialis xref: NCBITaxon:forma_specialis is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Fusarium oxysporum f. sp. cucumerinum (NCBITaxon:5508) is a forma specialis" created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -489,6 +492,7 @@ id: TAXRANK:0001006 name: serogroup xref: NCBITaxon:serogroup is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Neisseria meningitidis serogroup B (NCBITaxon:491) is a serogroup" created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -496,6 +500,7 @@ id: TAXRANK:0001007 name: genotype xref: NCBITaxon: genotype is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Hepatitis C virus genotype 4 (NCBITaxon:33745) is a genotype" created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -503,6 +508,7 @@ id: TAXRANK:0001008 name: biotype xref: NCBITaxon: biotype is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Haemophilus influenzae biotype aegyptius (NCBITaxon:725) is a biotype" created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -510,6 +516,7 @@ id: TAXRANK:0001009 name: morph xref: NCBITaxon:morph is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Acontias orientalis morph lineacauda (NCBITaxon:304407) is a morph" created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -517,6 +524,7 @@ id: TAXRANK:0001010 name: cohort xref: NCBITaxon:cohort is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Polyneoptera (NCBITaxon:33341) is a cohort" created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -524,6 +532,7 @@ id: TAXRANK:0001011 name: pathogroup xref: NCBITaxon:pathogroup is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Xanthomonas axonopodis subcluster 9.1 (NCBITaxon:1982676) is a pathogroup" created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -531,6 +540,7 @@ id: TAXRANK:0001012 name: subcohort xref: NCBITaxon:subcohort is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO_0000112 "Ostariophysi (NCBITaxon:32519) is a subcohort" created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] From 39b27f30e8a43bf9c8c8a8feb17b6caeb9d426c7 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 27 Nov 2024 20:39:23 +0100 Subject: [PATCH 3/9] Update taxrank-edit.obo --- src/ontology/taxrank-edit.obo | 36 ++++++++++++++++------------------- 1 file changed, 16 insertions(+), 20 deletions(-) diff --git a/src/ontology/taxrank-edit.obo b/src/ontology/taxrank-edit.obo index fb4c8a7..32184d8 100644 --- a/src/ontology/taxrank-edit.obo +++ b/src/ontology/taxrank-edit.obo @@ -446,13 +446,12 @@ def: "A token asserting that the taxon was not assigned a rank." [TAXRANK:curato is_a: TAXRANK:0000000 ! taxonomic_rank created_by: pmidford - [Term] id: TAXRANK:0001001 name: strain xref: NCBITaxon:strain is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Azotobacter chroococcum (strain mcd 1) (NCBITaxon:355) is a strain" +property_value: IAO:0000112 "Azotobacter chroococcum (strain mcd 1) (NCBITaxon:355) is a strain"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -460,7 +459,7 @@ id: TAXRANK:0001002 name: isolate xref: NCBITaxon:isolate is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Plasmodium falciparum FCR-3/Gambia (NCBITaxon:5838) is an isolate" +property_value: IAO:0000112 "Plasmodium falciparum FCR-3/Gambia (NCBITaxon:5838) is an isolate"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -468,7 +467,7 @@ id: TAXRANK:0001003 name: serotype xref: NCBITaxon:serotype is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Bovine adenovirus 3 (NCBITaxon:10510) is a serotype" +property_value: IAO:0000112 "Bovine adenovirus 3 (NCBITaxon:10510) is a serotype"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -476,7 +475,7 @@ id: TAXRANK:0001004 name: clade xref: NCBITaxon:clade is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Embryophyta (NCBITaxon:3193) is a clade" +property_value: IAO:0000112 "Embryophyta (NCBITaxon:3193) is a clade"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -484,7 +483,7 @@ id: TAXRANK:0001005 name: forma specialis xref: NCBITaxon:forma_specialis is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Fusarium oxysporum f. sp. cucumerinum (NCBITaxon:5508) is a forma specialis" +property_value: IAO:0000112 "Fusarium oxysporum f. sp. cucumerinum (NCBITaxon:5508) is a forma specialis"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -492,7 +491,7 @@ id: TAXRANK:0001006 name: serogroup xref: NCBITaxon:serogroup is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Neisseria meningitidis serogroup B (NCBITaxon:491) is a serogroup" +property_value: IAO:0000112 "Neisseria meningitidis serogroup B (NCBITaxon:491) is a serogroup"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -500,7 +499,7 @@ id: TAXRANK:0001007 name: genotype xref: NCBITaxon: genotype is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Hepatitis C virus genotype 4 (NCBITaxon:33745) is a genotype" +property_value: IAO:0000112 "Hepatitis C virus genotype 4 (NCBITaxon:33745) is a genotype"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -508,7 +507,7 @@ id: TAXRANK:0001008 name: biotype xref: NCBITaxon: biotype is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Haemophilus influenzae biotype aegyptius (NCBITaxon:725) is a biotype" +property_value: IAO:0000112 "Haemophilus influenzae biotype aegyptius (NCBITaxon:725) is a biotype"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -516,7 +515,7 @@ id: TAXRANK:0001009 name: morph xref: NCBITaxon:morph is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Acontias orientalis morph lineacauda (NCBITaxon:304407) is a morph" +property_value: IAO:0000112 "Acontias orientalis morph lineacauda (NCBITaxon:304407) is a morph"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -524,7 +523,7 @@ id: TAXRANK:0001010 name: cohort xref: NCBITaxon:cohort is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Polyneoptera (NCBITaxon:33341) is a cohort" +property_value: IAO:0000112 "Polyneoptera (NCBITaxon:33341) is a cohort"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -532,7 +531,7 @@ id: TAXRANK:0001011 name: pathogroup xref: NCBITaxon:pathogroup is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Xanthomonas axonopodis subcluster 9.1 (NCBITaxon:1982676) is a pathogroup" +property_value: IAO:0000112 "Xanthomonas axonopodis subcluster 9.1 (NCBITaxon:1982676) is a pathogroup"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -540,14 +539,7 @@ id: TAXRANK:0001012 name: subcohort xref: NCBITaxon:subcohort is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO_0000112 "Ostariophysi (NCBITaxon:32519) is a subcohort" -created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt - -[Term] -id: TAXRANK:0001013 -name: -xref: NCBITaxon: -is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Ostariophysi (NCBITaxon:32519) is a subcohort"^^xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Typedef] @@ -555,3 +547,7 @@ id: TAXRANK:1000000 name: has_rank is_metadata_tag: true +[Typedef] +id: IAO:0000112 +name: example of usage +is_metadata_tag: true From 0bd152b182b0af5927c1f5dfba5864aefa042425 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 27 Nov 2024 20:45:35 +0100 Subject: [PATCH 4/9] Update taxrank-edit.obo --- src/ontology/taxrank-edit.obo | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/src/ontology/taxrank-edit.obo b/src/ontology/taxrank-edit.obo index 32184d8..a0eb4ed 100644 --- a/src/ontology/taxrank-edit.obo +++ b/src/ontology/taxrank-edit.obo @@ -451,7 +451,7 @@ id: TAXRANK:0001001 name: strain xref: NCBITaxon:strain is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Azotobacter chroococcum (strain mcd 1) (NCBITaxon:355) is a strain"^^xsd:string +property_value: IAO:0000112 "Azotobacter chroococcum (strain mcd 1) (NCBITaxon:355) is a strain" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -459,7 +459,7 @@ id: TAXRANK:0001002 name: isolate xref: NCBITaxon:isolate is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Plasmodium falciparum FCR-3/Gambia (NCBITaxon:5838) is an isolate"^^xsd:string +property_value: IAO:0000112 "Plasmodium falciparum FCR-3/Gambia (NCBITaxon:5838) is an isolate" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -467,7 +467,7 @@ id: TAXRANK:0001003 name: serotype xref: NCBITaxon:serotype is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Bovine adenovirus 3 (NCBITaxon:10510) is a serotype"^^xsd:string +property_value: IAO:0000112 "Bovine adenovirus 3 (NCBITaxon:10510) is a serotype" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -475,7 +475,7 @@ id: TAXRANK:0001004 name: clade xref: NCBITaxon:clade is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Embryophyta (NCBITaxon:3193) is a clade"^^xsd:string +property_value: IAO:0000112 "Embryophyta (NCBITaxon:3193) is a clade" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -483,7 +483,7 @@ id: TAXRANK:0001005 name: forma specialis xref: NCBITaxon:forma_specialis is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Fusarium oxysporum f. sp. cucumerinum (NCBITaxon:5508) is a forma specialis"^^xsd:string +property_value: IAO:0000112 "Fusarium oxysporum f. sp. cucumerinum (NCBITaxon:5508) is a forma specialis" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -491,23 +491,23 @@ id: TAXRANK:0001006 name: serogroup xref: NCBITaxon:serogroup is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Neisseria meningitidis serogroup B (NCBITaxon:491) is a serogroup"^^xsd:string +property_value: IAO:0000112 "Neisseria meningitidis serogroup B (NCBITaxon:491) is a serogroup" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] id: TAXRANK:0001007 name: genotype -xref: NCBITaxon: genotype +xref: NCBITaxon:genotype is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Hepatitis C virus genotype 4 (NCBITaxon:33745) is a genotype"^^xsd:string +property_value: IAO:0000112 "Hepatitis C virus genotype 4 (NCBITaxon:33745) is a genotype" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] id: TAXRANK:0001008 name: biotype -xref: NCBITaxon: biotype +xref: NCBITaxon:biotype is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Haemophilus influenzae biotype aegyptius (NCBITaxon:725) is a biotype"^^xsd:string +property_value: IAO:0000112 "Haemophilus influenzae biotype aegyptius (NCBITaxon:725) is a biotype" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -515,7 +515,7 @@ id: TAXRANK:0001009 name: morph xref: NCBITaxon:morph is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Acontias orientalis morph lineacauda (NCBITaxon:304407) is a morph"^^xsd:string +property_value: IAO:0000112 "Acontias orientalis morph lineacauda (NCBITaxon:304407) is a morph" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -523,7 +523,7 @@ id: TAXRANK:0001010 name: cohort xref: NCBITaxon:cohort is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Polyneoptera (NCBITaxon:33341) is a cohort"^^xsd:string +property_value: IAO:0000112 "Polyneoptera (NCBITaxon:33341) is a cohort" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -531,7 +531,7 @@ id: TAXRANK:0001011 name: pathogroup xref: NCBITaxon:pathogroup is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Xanthomonas axonopodis subcluster 9.1 (NCBITaxon:1982676) is a pathogroup"^^xsd:string +property_value: IAO:0000112 "Xanthomonas axonopodis subcluster 9.1 (NCBITaxon:1982676) is a pathogroup" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -539,7 +539,7 @@ id: TAXRANK:0001012 name: subcohort xref: NCBITaxon:subcohort is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Ostariophysi (NCBITaxon:32519) is a subcohort"^^xsd:string +property_value: IAO:0000112 "Ostariophysi (NCBITaxon:32519) is a subcohort" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Typedef] From 930fc2c0d63bae68c8828874af7f3c68248ed465 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 27 Nov 2024 20:48:21 +0100 Subject: [PATCH 5/9] Update taxrank-edit.obo --- src/ontology/taxrank-edit.obo | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/src/ontology/taxrank-edit.obo b/src/ontology/taxrank-edit.obo index a0eb4ed..7472a91 100644 --- a/src/ontology/taxrank-edit.obo +++ b/src/ontology/taxrank-edit.obo @@ -451,7 +451,7 @@ id: TAXRANK:0001001 name: strain xref: NCBITaxon:strain is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Azotobacter chroococcum (strain mcd 1) (NCBITaxon:355) is a strain" xsd:string +property_value: IAO:0000112 "Azotobacter chroococcum (strain mcd 1) (NCBITaxon:355) has rank strain" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -467,7 +467,7 @@ id: TAXRANK:0001003 name: serotype xref: NCBITaxon:serotype is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Bovine adenovirus 3 (NCBITaxon:10510) is a serotype" xsd:string +property_value: IAO:0000112 "Bovine adenovirus 3 (NCBITaxon:10510) has rank serotype" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -475,7 +475,7 @@ id: TAXRANK:0001004 name: clade xref: NCBITaxon:clade is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Embryophyta (NCBITaxon:3193) is a clade" xsd:string +property_value: IAO:0000112 "Embryophyta (NCBITaxon:3193) has rank clade" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -483,7 +483,7 @@ id: TAXRANK:0001005 name: forma specialis xref: NCBITaxon:forma_specialis is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Fusarium oxysporum f. sp. cucumerinum (NCBITaxon:5508) is a forma specialis" xsd:string +property_value: IAO:0000112 "Fusarium oxysporum f. sp. cucumerinum (NCBITaxon:5508) has rank forma specialis" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -491,7 +491,7 @@ id: TAXRANK:0001006 name: serogroup xref: NCBITaxon:serogroup is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Neisseria meningitidis serogroup B (NCBITaxon:491) is a serogroup" xsd:string +property_value: IAO:0000112 "Neisseria meningitidis serogroup B (NCBITaxon:491) has rank serogroup" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -499,7 +499,7 @@ id: TAXRANK:0001007 name: genotype xref: NCBITaxon:genotype is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Hepatitis C virus genotype 4 (NCBITaxon:33745) is a genotype" xsd:string +property_value: IAO:0000112 "Hepatitis C virus genotype 4 (NCBITaxon:33745) has rank genotype" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -507,7 +507,7 @@ id: TAXRANK:0001008 name: biotype xref: NCBITaxon:biotype is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Haemophilus influenzae biotype aegyptius (NCBITaxon:725) is a biotype" xsd:string +property_value: IAO:0000112 "Haemophilus influenzae biotype aegyptius (NCBITaxon:725) has rank biotype" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -515,7 +515,7 @@ id: TAXRANK:0001009 name: morph xref: NCBITaxon:morph is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Acontias orientalis morph lineacauda (NCBITaxon:304407) is a morph" xsd:string +property_value: IAO:0000112 "Acontias orientalis morph lineacauda (NCBITaxon:304407) has rank morph" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -523,7 +523,7 @@ id: TAXRANK:0001010 name: cohort xref: NCBITaxon:cohort is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Polyneoptera (NCBITaxon:33341) is a cohort" xsd:string +property_value: IAO:0000112 "Polyneoptera (NCBITaxon:33341) has rank cohort" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -531,7 +531,7 @@ id: TAXRANK:0001011 name: pathogroup xref: NCBITaxon:pathogroup is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Xanthomonas axonopodis subcluster 9.1 (NCBITaxon:1982676) is a pathogroup" xsd:string +property_value: IAO:0000112 "Xanthomonas axonopodis subcluster 9.1 (NCBITaxon:1982676) has rank pathogroup" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Term] @@ -539,7 +539,7 @@ id: TAXRANK:0001012 name: subcohort xref: NCBITaxon:subcohort is_a: TAXRANK:0000000 ! taxonomic_rank -property_value: IAO:0000112 "Ostariophysi (NCBITaxon:32519) is a subcohort" xsd:string +property_value: IAO:0000112 "Ostariophysi (NCBITaxon:32519) has rank subcohort" xsd:string created_by: orcid:0000-0003-4423-4370 ! Charles Tapley Hoyt [Typedef] From 0527d24345316b38d1167dc95b7f7ced80a74072 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 28 Nov 2024 02:30:18 +0100 Subject: [PATCH 6/9] Add releases --- taxrank.obo | 106 ++++++- taxrank.owl | 874 +++++++++++++++++++++++++++++++--------------------- 2 files changed, 633 insertions(+), 347 deletions(-) diff --git a/taxrank.obo b/taxrank.obo index 519afa2..f994525 100644 --- a/taxrank.obo +++ b/taxrank.obo @@ -1,9 +1,10 @@ format-version: 1.2 -data-version: releases/2016-04-15 +data-version: releases/2024-11-28 default-namespace: taxonomic_rank +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# remark: To the extent possible under law, Peter E. Midford has waived all copyright and related or neighboring rights to the Taxonomic Rank Vocabulary (TAXRANK). This work is published from the United States. It is requested that users of this vocabulary cite it at the following URI: http://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary ontology: taxrank -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nSubClassOf( owl:Thing)\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\n############################\n# Classes\n############################\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n\n) [Term] id: TAXRANK:0000000 @@ -447,6 +448,107 @@ def: "A token asserting that the taxon was not assigned a rank." [TAXRANK:curato is_a: TAXRANK:0000000 ! taxonomic_rank created_by: pmidford +[Term] +id: TAXRANK:0001001 +name: strain +xref: NCBITaxon:strain +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Azotobacter chroococcum (strain mcd 1) (NCBITaxon:355) has rank strain" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Term] +id: TAXRANK:0001002 +name: isolate +xref: NCBITaxon:isolate +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Plasmodium falciparum FCR-3/Gambia (NCBITaxon:5838) is an isolate" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Term] +id: TAXRANK:0001003 +name: serotype +xref: NCBITaxon:serotype +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Bovine adenovirus 3 (NCBITaxon:10510) has rank serotype" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Term] +id: TAXRANK:0001004 +name: clade +xref: NCBITaxon:clade +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Embryophyta (NCBITaxon:3193) has rank clade" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Term] +id: TAXRANK:0001005 +name: forma specialis +xref: NCBITaxon:forma_specialis +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Fusarium oxysporum f. sp. cucumerinum (NCBITaxon:5508) has rank forma specialis" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Term] +id: TAXRANK:0001006 +name: serogroup +xref: NCBITaxon:serogroup +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Neisseria meningitidis serogroup B (NCBITaxon:491) has rank serogroup" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Term] +id: TAXRANK:0001007 +name: genotype +xref: NCBITaxon:genotype +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Hepatitis C virus genotype 4 (NCBITaxon:33745) has rank genotype" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Term] +id: TAXRANK:0001008 +name: biotype +xref: NCBITaxon:biotype +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Haemophilus influenzae biotype aegyptius (NCBITaxon:725) has rank biotype" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Term] +id: TAXRANK:0001009 +name: morph +xref: NCBITaxon:morph +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Acontias orientalis morph lineacauda (NCBITaxon:304407) has rank morph" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Term] +id: TAXRANK:0001010 +name: cohort +xref: NCBITaxon:cohort +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Polyneoptera (NCBITaxon:33341) has rank cohort" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Term] +id: TAXRANK:0001011 +name: pathogroup +xref: NCBITaxon:pathogroup +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Xanthomonas axonopodis subcluster 9.1 (NCBITaxon:1982676) has rank pathogroup" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Term] +id: TAXRANK:0001012 +name: subcohort +xref: NCBITaxon:subcohort +is_a: TAXRANK:0000000 ! taxonomic_rank +property_value: IAO:0000112 "Ostariophysi (NCBITaxon:32519) has rank subcohort" xsd:string +created_by: orcid:0000-0003-4423-4370 + +[Typedef] +id: IAO:0000112 +name: example of usage +is_metadata_tag: true + [Typedef] id: TAXRANK:1000000 name: has_rank diff --git a/taxrank.owl b/taxrank.owl index 7ec7b8e..10d12cc 100644 --- a/taxrank.owl +++ b/taxrank.owl @@ -1,17 +1,18 @@ + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - 1.2 - To the extent possible under law, Peter E. Midford has waived all copyright and related or neighboring rights to the Taxonomic Rank Vocabulary (TAXRANK). This work is published from the United States. It is requested that users of this vocabulary cite it at the following URI: http://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary - taxonomic_rank - + + taxonomic_rank + 1.2 + To the extent possible under law, Peter E. Midford has waived all copyright and related or neighboring rights to the Taxonomic Rank Vocabulary (TAXRANK). This work is published from the United States. It is requested that users of this vocabulary cite it at the following URI: http://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary @@ -27,10 +28,21 @@ + + + + taxonomic_rank + IAO:0000112 + true + example of usage + + + + - definition + definition @@ -38,17 +50,19 @@ - has_rank - TAXRANK:1000000 - taxonomic_rank + taxonomic_rank + TAXRANK:1000000 true + has_rank - + + created by + @@ -61,7 +75,7 @@ - database_cross_reference + database_cross_reference @@ -69,7 +83,7 @@ - has_exact_synonym + has_exact_synonym @@ -77,7 +91,7 @@ - has_obo_format_version + has_obo_format_version @@ -85,14 +99,16 @@ - has_obo_namespace + has_obo_namespace - + + id + @@ -122,17 +138,17 @@ - taxonomic_rank - A level of depth of a taxon in a taxonomic hierarchy. - TAXRANK:0000000 - taxonomic_rank + A level of depth of a taxon in a taxonomic hierarchy. + taxonomic_rank + TAXRANK:0000000 + taxonomic_rank - A level of depth of a taxon in a taxonomic hierarchy. - TAXRANK:curator - + + A level of depth of a taxon in a taxonomic hierarchy. + TAXRANK:curator @@ -140,13 +156,13 @@ - phylum - NCBITaxon:phylum - TAXRANK:0000001 - division - http://rs.tdwg.org/ontology/voc/TaxonRank#Phylum - taxonomic_rank + NCBITaxon:phylum + http://rs.tdwg.org/ontology/voc/TaxonRank#Phylum + division + taxonomic_rank + TAXRANK:0000001 + phylum @@ -154,12 +170,12 @@ - class - NCBITaxon:class - TAXRANK:0000002 - http://rs.tdwg.org/ontology/voc/TaxonRank#Class - taxonomic_rank + NCBITaxon:class + http://rs.tdwg.org/ontology/voc/TaxonRank#Class + taxonomic_rank + TAXRANK:0000002 + class @@ -167,12 +183,12 @@ - order - NCBITaxon:order - TAXRANK:0000003 - http://rs.tdwg.org/ontology/voc/TaxonRank#Order - taxonomic_rank + NCBITaxon:order + http://rs.tdwg.org/ontology/voc/TaxonRank#Order + taxonomic_rank + TAXRANK:0000003 + order @@ -180,12 +196,12 @@ - family - NCBITaxon:family - TAXRANK:0000004 - http://rs.tdwg.org/ontology/voc/TaxonRank#Family - taxonomic_rank + NCBITaxon:family + http://rs.tdwg.org/ontology/voc/TaxonRank#Family + taxonomic_rank + TAXRANK:0000004 + family @@ -193,12 +209,12 @@ - genus - NCBITaxon:genus - TAXRANK:0000005 - http://rs.tdwg.org/ontology/voc/TaxonRank#Genus - taxonomic_rank + NCBITaxon:genus + http://rs.tdwg.org/ontology/voc/TaxonRank#Genus + taxonomic_rank + TAXRANK:0000005 + genus @@ -206,12 +222,12 @@ - species - NCBITaxon:species - TAXRANK:0000006 - http://rs.tdwg.org/ontology/voc/TaxonRank#Species - taxonomic_rank + NCBITaxon:species + http://rs.tdwg.org/ontology/voc/TaxonRank#Species + taxonomic_rank + TAXRANK:0000006 + species @@ -219,12 +235,12 @@ - subclass - NCBITaxon:subclass - TAXRANK:0000007 - http://rs.tdwg.org/ontology/voc/TaxonRank#Subclass - taxonomic_rank + NCBITaxon:subclass + http://rs.tdwg.org/ontology/voc/TaxonRank#Subclass + taxonomic_rank + TAXRANK:0000007 + subclass @@ -232,13 +248,13 @@ - subphylum - NCBITaxon:subphylum - TAXRANK:0000008 - http://rs.tdwg.org/ontology/voc/TaxonRank#SubPhylum - subdivision - taxonomic_rank + NCBITaxon:subphylum + http://rs.tdwg.org/ontology/voc/TaxonRank#SubPhylum + subdivision + taxonomic_rank + TAXRANK:0000008 + subphylum @@ -246,12 +262,12 @@ - subgenus - NCBITaxon:subgenus - TAXRANK:0000009 - http://rs.tdwg.org/ontology/voc/TaxonRank#Subgenus - taxonomic_rank + NCBITaxon:subgenus + http://rs.tdwg.org/ontology/voc/TaxonRank#Subgenus + taxonomic_rank + TAXRANK:0000009 + subgenus @@ -259,11 +275,11 @@ - species_group - NCBITaxon:species_group - TAXRANK:0000010 - taxonomic_rank + NCBITaxon:species_group + taxonomic_rank + TAXRANK:0000010 + species_group @@ -271,12 +287,12 @@ - species_subgroup - NCBITaxon:species_subgroup - TAXRANK:0000011 - species complex - taxonomic_rank + NCBITaxon:species_subgroup + species complex + taxonomic_rank + TAXRANK:0000011 + species_subgroup @@ -284,10 +300,10 @@ - species_complex - TAXRANK:0000012 - taxonomic_rank + taxonomic_rank + TAXRANK:0000012 + species_complex @@ -295,12 +311,12 @@ - infraorder - NCBITaxon:infraorder - TAXRANK:0000013 - http://rs.tdwg.org/ontology/voc/TaxonRank#Infraorder - taxonomic_rank + NCBITaxon:infraorder + http://rs.tdwg.org/ontology/voc/TaxonRank#Infraorder + taxonomic_rank + TAXRANK:0000013 + infraorder @@ -308,13 +324,13 @@ - suborder - NCBITaxon:suborder - TAXRANK:0000014 - http://rs.tdwg.org/ontology/voc/TaxonRank#Suborder - pmidford - taxonomic_rank + pmidford + NCBITaxon:suborder + http://rs.tdwg.org/ontology/voc/TaxonRank#Suborder + taxonomic_rank + TAXRANK:0000014 + suborder @@ -322,13 +338,13 @@ - superclass - NCBITaxon:superclass - TAXRANK:0000015 - http://rs.tdwg.org/ontology/voc/TaxonRank#Superclass - pmidford - taxonomic_rank + pmidford + NCBITaxon:superclass + http://rs.tdwg.org/ontology/voc/TaxonRank#Superclass + taxonomic_rank + TAXRANK:0000015 + superclass @@ -336,13 +352,13 @@ - varietas - NCBITaxon:varietas - TAXRANK:0000016 - pmidford - taxonomic_rank - variety + pmidford + NCBITaxon:varietas + variety + taxonomic_rank + TAXRANK:0000016 + varietas @@ -350,13 +366,13 @@ - kingdom - NCBITaxon:kingdom - TAXRANK:0000017 - http://rs.tdwg.org/ontology/voc/TaxonRank#Kingdom - pmidford - taxonomic_rank + pmidford + NCBITaxon:kingdom + http://rs.tdwg.org/ontology/voc/TaxonRank#Kingdom + taxonomic_rank + TAXRANK:0000017 + kingdom @@ -364,13 +380,13 @@ - superfamily - NCBITaxon:superfamily - TAXRANK:0000018 - http://rs.tdwg.org/ontology/voc/TaxonRank#Superfamily - pmidford - taxonomic_rank + pmidford + NCBITaxon:superfamily + http://rs.tdwg.org/ontology/voc/TaxonRank#Superfamily + taxonomic_rank + TAXRANK:0000018 + superfamily @@ -378,13 +394,13 @@ - infraclass - NCBITaxon:infraclass - TAXRANK:0000019 - http://rs.tdwg.org/ontology/voc/TaxonRank#Infraclass - pmidford - taxonomic_rank + pmidford + NCBITaxon:infraclass + http://rs.tdwg.org/ontology/voc/TaxonRank#Infraclass + taxonomic_rank + TAXRANK:0000019 + infraclass @@ -392,13 +408,13 @@ - superorder - NCBITaxon:superorder - TAXRANK:0000020 - http://rs.tdwg.org/ontology/voc/TaxonRank#Superorder - pmidford - taxonomic_rank + pmidford + NCBITaxon:superorder + http://rs.tdwg.org/ontology/voc/TaxonRank#Superorder + taxonomic_rank + TAXRANK:0000020 + superorder @@ -406,12 +422,12 @@ - parvorder - NCBITaxon:parvorder - TAXRANK:0000021 - pmidford - taxonomic_rank + pmidford + NCBITaxon:parvorder + taxonomic_rank + TAXRANK:0000021 + parvorder @@ -419,13 +435,13 @@ - superkingdom - NCBITaxon:superkingdom - TAXRANK:0000022 - http://rs.tdwg.org/ontology/voc/TaxonRank#Superkingdom - pmidford - taxonomic_rank + pmidford + NCBITaxon:superkingdom + http://rs.tdwg.org/ontology/voc/TaxonRank#Superkingdom + taxonomic_rank + TAXRANK:0000022 + superkingdom @@ -433,13 +449,13 @@ - subspecies - NCBITaxon:subspecies - TAXRANK:0000023 - http://rs.tdwg.org/ontology/voc/TaxonRank#Subspecies - pmidford - taxonomic_rank + pmidford + NCBITaxon:subspecies + http://rs.tdwg.org/ontology/voc/TaxonRank#Subspecies + taxonomic_rank + TAXRANK:0000023 + subspecies @@ -447,13 +463,13 @@ - subfamily - NCBITaxon:subfamily - TAXRANK:0000024 - http://rs.tdwg.org/ontology/voc/TaxonRank#Subfamily - pmidford - taxonomic_rank + pmidford + NCBITaxon:subfamily + http://rs.tdwg.org/ontology/voc/TaxonRank#Subfamily + taxonomic_rank + TAXRANK:0000024 + subfamily @@ -461,13 +477,13 @@ - tribe - NCBITaxon:tribe - TAXRANK:0000025 - http://rs.tdwg.org/ontology/voc/TaxonRank#Tribe - pmidford - taxonomic_rank + pmidford + NCBITaxon:tribe + http://rs.tdwg.org/ontology/voc/TaxonRank#Tribe + taxonomic_rank + TAXRANK:0000025 + tribe @@ -475,14 +491,14 @@ - forma - NCBITaxon:forma - TAXRANK:0000026 - form - http://rs.tdwg.org/ontology/voc/TaxonRank#Form - pmidford - taxonomic_rank + pmidford + NCBITaxon:forma + http://rs.tdwg.org/ontology/voc/TaxonRank#Form + form + taxonomic_rank + TAXRANK:0000026 + forma @@ -490,14 +506,14 @@ - superphylum - NCBITaxon:superphylum - TAXRANK:0000027 - http://rs.tdwg.org/ontology/voc/TaxonRank#Superphylum - pmidford - superdivision - taxonomic_rank + pmidford + NCBITaxon:superphylum + http://rs.tdwg.org/ontology/voc/TaxonRank#Superphylum + superdivision + taxonomic_rank + TAXRANK:0000027 + superphylum @@ -505,13 +521,13 @@ - subtribe - NCBITaxon:subtribe - TAXRANK:0000028 - http://rs.tdwg.org/ontology/voc/TaxonRank#Subtribe - pmidford - taxonomic_rank + pmidford + NCBITaxon:subtribe + http://rs.tdwg.org/ontology/voc/TaxonRank#Subtribe + taxonomic_rank + TAXRANK:0000028 + subtribe @@ -519,13 +535,13 @@ - subkingdom - NCBITaxon:subkingdom - TAXRANK:0000029 - http://rs.tdwg.org/ontology/voc/TaxonRank#Subkingdom - pmidford - taxonomic_rank + pmidford + NCBITaxon:subkingdom + http://rs.tdwg.org/ontology/voc/TaxonRank#Subkingdom + taxonomic_rank + TAXRANK:0000029 + subkingdom @@ -533,12 +549,12 @@ - section - TAXRANK:0000030 - http://rs.tdwg.org/ontology/voc/TaxonRank#Section - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Section + taxonomic_rank + TAXRANK:0000030 + section @@ -546,12 +562,12 @@ - series - TAXRANK:0000031 - http://rs.tdwg.org/ontology/voc/TaxonRank#Series - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Series + taxonomic_rank + TAXRANK:0000031 + series @@ -559,12 +575,12 @@ - bio-variety - TAXRANK:0000032 - http://rs.tdwg.org/ontology/voc/TaxonRank#Bio-variety - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Bio-variety + taxonomic_rank + TAXRANK:0000032 + bio-variety @@ -572,12 +588,12 @@ - candidate - TAXRANK:0000033 - http://rs.tdwg.org/ontology/voc/TaxonRank#Candidate - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Candidate + taxonomic_rank + TAXRANK:0000033 + candidate @@ -585,12 +601,12 @@ - cultivar - TAXRANK:0000034 - http://rs.tdwg.org/ontology/voc/TaxonRank#Cultivar - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Cultivar + taxonomic_rank + TAXRANK:0000034 + cultivar @@ -598,12 +614,12 @@ - cultivar-group - TAXRANK:0000035 - http://rs.tdwg.org/ontology/voc/TaxonRank#Cultivar-group - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Cultivar-group + taxonomic_rank + TAXRANK:0000035 + cultivar-group @@ -611,12 +627,12 @@ - denominationclass - TAXRANK:0000036 - http://rs.tdwg.org/ontology/voc/TaxonRank#DenominationClass - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#DenominationClass + taxonomic_rank + TAXRANK:0000036 + denominationclass @@ -624,13 +640,13 @@ - domain - TAXRANK:0000037 - empire - http://rs.tdwg.org/ontology/voc/TaxonRank#Domain - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Domain + empire + taxonomic_rank + TAXRANK:0000037 + domain @@ -638,12 +654,12 @@ - graft-chimaera - TAXRANK:0000038 - http://rs.tdwg.org/ontology/voc/TaxonRank#Graft-chimaera - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Graft-chimaera + taxonomic_rank + TAXRANK:0000038 + graft-chimaera @@ -651,12 +667,12 @@ - grex - TAXRANK:0000039 - http://rs.tdwg.org/ontology/voc/TaxonRank#Grex - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Grex + taxonomic_rank + TAXRANK:0000039 + grex @@ -664,13 +680,13 @@ - infraphylum - TAXRANK:0000040 - http://rs.tdwg.org/ontology/voc/TaxonRank#Infraphylum - infradivision - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Infraphylum + infradivision + taxonomic_rank + TAXRANK:0000040 + infraphylum @@ -678,12 +694,12 @@ - infrafamily - TAXRANK:0000041 - http://rs.tdwg.org/ontology/voc/TaxonRank#Infrafamily - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Infrafamily + taxonomic_rank + TAXRANK:0000041 + infrafamily @@ -691,12 +707,12 @@ - infragenerictaxon - TAXRANK:0000042 - http://rs.tdwg.org/ontology/voc/TaxonRank#InfragenericTaxon - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#InfragenericTaxon + taxonomic_rank + TAXRANK:0000042 + infragenerictaxon @@ -704,12 +720,12 @@ - infragenus - TAXRANK:0000043 - http://rs.tdwg.org/ontology/voc/TaxonRank#Infragenus - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Infragenus + taxonomic_rank + TAXRANK:0000043 + infragenus @@ -717,12 +733,12 @@ - infrakingdom - TAXRANK:0000044 - http://rs.tdwg.org/ontology/voc/TaxonRank#Infrakingdom - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Infrakingdom + taxonomic_rank + TAXRANK:0000044 + infrakingdom @@ -730,12 +746,12 @@ - infraspecies - TAXRANK:0000045 - http://rs.tdwg.org/ontology/voc/TaxonRank#Infraspecies - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Infraspecies + taxonomic_rank + TAXRANK:0000045 + infraspecies @@ -743,12 +759,12 @@ - infraspecificTaxon - TAXRANK:0000046 - http://rs.tdwg.org/ontology/voc/TaxonRank#InfraspecificTaxon - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#InfraspecificTaxon + taxonomic_rank + TAXRANK:0000046 + infraspecificTaxon @@ -756,12 +772,12 @@ - infratribe - TAXRANK:0000047 - http://rs.tdwg.org/ontology/voc/TaxonRank#Infratribe - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Infratribe + taxonomic_rank + TAXRANK:0000047 + infratribe @@ -769,12 +785,12 @@ - patho-variety - TAXRANK:0000048 - http://rs.tdwg.org/ontology/voc/TaxonRank#patho-variety - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#patho-variety + taxonomic_rank + TAXRANK:0000048 + patho-variety @@ -782,12 +798,12 @@ - specialform - TAXRANK:0000049 - http://rs.tdwg.org/ontology/voc/TaxonRank#Specialform - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Specialform + taxonomic_rank + TAXRANK:0000049 + specialform @@ -795,12 +811,12 @@ - speciesaggregate - TAXRANK:0000050 - http://rs.tdwg.org/ontology/voc/TaxonRank#SpeciesAggregate - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#SpeciesAggregate + taxonomic_rank + TAXRANK:0000050 + speciesaggregate @@ -808,12 +824,12 @@ - subvariety - TAXRANK:0000051 - http://rs.tdwg.org/ontology/voc/TaxonRank#Sub-Variety - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Sub-Variety + taxonomic_rank + TAXRANK:0000051 + subvariety @@ -821,12 +837,12 @@ - subsubvariety - TAXRANK:0000052 - http://rs.tdwg.org/ontology/voc/TaxonRank#Sub-Sub-Variety - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Sub-Sub-Variety + taxonomic_rank + TAXRANK:0000052 + subsubvariety @@ -834,12 +850,12 @@ - subsection - TAXRANK:0000053 - http://rs.tdwg.org/ontology/voc/TaxonRank#Subsection - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Subsection + taxonomic_rank + TAXRANK:0000053 + subsection @@ -847,12 +863,12 @@ - subseries - TAXRANK:0000054 - http://rs.tdwg.org/ontology/voc/TaxonRank#Subseries - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Subseries + taxonomic_rank + TAXRANK:0000054 + subseries @@ -860,12 +876,12 @@ - subspecificaggregate - TAXRANK:0000055 - http://rs.tdwg.org/ontology/voc/TaxonRank#SubspecificAggregate - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#SubspecificAggregate + taxonomic_rank + TAXRANK:0000055 + subspecificaggregate @@ -873,12 +889,12 @@ - subsubform - TAXRANK:0000056 - http://rs.tdwg.org/ontology/voc/TaxonRank#Subsubform - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Subsubform + taxonomic_rank + TAXRANK:0000056 + subsubform @@ -886,12 +902,12 @@ - supertribe - TAXRANK:0000057 - http://rs.tdwg.org/ontology/voc/TaxonRank#Supertribe - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#Supertribe + taxonomic_rank + TAXRANK:0000057 + supertribe @@ -899,12 +915,12 @@ - supragenerictaxon - TAXRANK:0000058 - http://rs.tdwg.org/ontology/voc/TaxonRank#SupragenericTaxon - pmidford - taxonomic_rank + pmidford + http://rs.tdwg.org/ontology/voc/TaxonRank#SupragenericTaxon + taxonomic_rank + TAXRANK:0000058 + supragenerictaxon @@ -912,11 +928,11 @@ - subform - TAXRANK:0000059 - pmidford - taxonomic_rank + pmidford + taxonomic_rank + TAXRANK:0000059 + subform @@ -924,22 +940,190 @@ - no_rank - A token asserting that the taxon was not assigned a rank. - TAXRANK:0000060 - pmidford - taxonomic_rank + A token asserting that the taxon was not assigned a rank. + pmidford + taxonomic_rank + TAXRANK:0000060 + no_rank - A token asserting that the taxon was not assigned a rank. - TAXRANK:curator - + + A token asserting that the taxon was not assigned a rank. + TAXRANK:curator + + + + + + + + Azotobacter chroococcum (strain mcd 1) (NCBITaxon:355) has rank strain + orcid:0000-0003-4423-4370 + NCBITaxon:strain + taxonomic_rank + TAXRANK:0001001 + strain + + + + + + + + + Plasmodium falciparum FCR-3/Gambia (NCBITaxon:5838) is an isolate + orcid:0000-0003-4423-4370 + NCBITaxon:isolate + taxonomic_rank + TAXRANK:0001002 + isolate + + + + + + + + + Bovine adenovirus 3 (NCBITaxon:10510) has rank serotype + orcid:0000-0003-4423-4370 + NCBITaxon:serotype + taxonomic_rank + TAXRANK:0001003 + serotype + + + + + + + + + Embryophyta (NCBITaxon:3193) has rank clade + orcid:0000-0003-4423-4370 + NCBITaxon:clade + taxonomic_rank + TAXRANK:0001004 + clade + + + + + + + + + Fusarium oxysporum f. sp. cucumerinum (NCBITaxon:5508) has rank forma specialis + orcid:0000-0003-4423-4370 + NCBITaxon:forma_specialis + taxonomic_rank + TAXRANK:0001005 + forma specialis + + + + + + + + + Neisseria meningitidis serogroup B (NCBITaxon:491) has rank serogroup + orcid:0000-0003-4423-4370 + NCBITaxon:serogroup + taxonomic_rank + TAXRANK:0001006 + serogroup + + + + + + + + + Hepatitis C virus genotype 4 (NCBITaxon:33745) has rank genotype + orcid:0000-0003-4423-4370 + NCBITaxon:genotype + taxonomic_rank + TAXRANK:0001007 + genotype + + + + + + + + + Haemophilus influenzae biotype aegyptius (NCBITaxon:725) has rank biotype + orcid:0000-0003-4423-4370 + NCBITaxon:biotype + taxonomic_rank + TAXRANK:0001008 + biotype + + + + + + + + + Acontias orientalis morph lineacauda (NCBITaxon:304407) has rank morph + orcid:0000-0003-4423-4370 + NCBITaxon:morph + taxonomic_rank + TAXRANK:0001009 + morph + + + + + + + + + Polyneoptera (NCBITaxon:33341) has rank cohort + orcid:0000-0003-4423-4370 + NCBITaxon:cohort + taxonomic_rank + TAXRANK:0001010 + cohort + + + + + + + + + Xanthomonas axonopodis subcluster 9.1 (NCBITaxon:1982676) has rank pathogroup + orcid:0000-0003-4423-4370 + NCBITaxon:pathogroup + taxonomic_rank + TAXRANK:0001011 + pathogroup + + + + + + + + + Ostariophysi (NCBITaxon:32519) has rank subcohort + orcid:0000-0003-4423-4370 + NCBITaxon:subcohort + taxonomic_rank + TAXRANK:0001012 + subcohort + - + From 4f295a37b1ce7f7388b83f55091ab294f7198ac9 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 28 Nov 2024 02:44:39 +0100 Subject: [PATCH 7/9] Cleanup of property values and attribution --- src/ontology/taxrank-edit.obo | 5 +++++ taxrank.obo | 5 +++++ taxrank.owl | 12 +++++++++++- 3 files changed, 21 insertions(+), 1 deletion(-) diff --git a/src/ontology/taxrank-edit.obo b/src/ontology/taxrank-edit.obo index 7472a91..7c11b4a 100644 --- a/src/ontology/taxrank-edit.obo +++ b/src/ontology/taxrank-edit.obo @@ -3,6 +3,10 @@ data-version: 2013-11-10 default-namespace: taxonomic_rank remark: To the extent possible under law, Peter E. Midford has waived all copyright and related or neighboring rights to the Taxonomic Rank Vocabulary (TAXRANK). This work is published from the United States. It is requested that users of this vocabulary cite it at the following URI: http://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary ontology: taxrank +idspace: dcterms http://purl.org/dc/terms/ +idspace: orcid https://orcid.org/ +property_value: dcterms:contributor orcid:0000-0001-6512-3296 +property_value: dcterms:contributor orcid:0000-0003-4423-4370 [Term] id: TAXRANK:0000000 @@ -551,3 +555,4 @@ is_metadata_tag: true id: IAO:0000112 name: example of usage is_metadata_tag: true +namespace: iao diff --git a/taxrank.obo b/taxrank.obo index f994525..3f52f17 100644 --- a/taxrank.obo +++ b/taxrank.obo @@ -1,9 +1,13 @@ format-version: 1.2 data-version: releases/2024-11-28 default-namespace: taxonomic_rank +idspace: dcterms http://purl.org/dc/terms/ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: orcid https://orcid.org/ remark: To the extent possible under law, Peter E. Midford has waived all copyright and related or neighboring rights to the Taxonomic Rank Vocabulary (TAXRANK). This work is published from the United States. It is requested that users of this vocabulary cite it at the following URI: http://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary ontology: taxrank +property_value: dcterms:contributor orcid:0000-0001-6512-3296 +property_value: dcterms:contributor orcid:0000-0003-4423-4370 owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\n############################\n# Classes\n############################\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n\n) [Term] @@ -547,6 +551,7 @@ created_by: orcid:0000-0003-4423-4370 [Typedef] id: IAO:0000112 name: example of usage +namespace: iao is_metadata_tag: true [Typedef] diff --git a/taxrank.owl b/taxrank.owl index 10d12cc..3b2963c 100644 --- a/taxrank.owl +++ b/taxrank.owl @@ -7,9 +7,13 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:orcid="https://orcid.org/" + xmlns:dcterms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + taxonomic_rank 1.2 To the extent possible under law, Peter E. Midford has waived all copyright and related or neighboring rights to the Taxonomic Rank Vocabulary (TAXRANK). This work is published from the United States. It is requested that users of this vocabulary cite it at the following URI: http://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary @@ -31,7 +35,7 @@ - taxonomic_rank + iao IAO:0000112 true example of usage @@ -58,6 +62,12 @@ + + + + + + From cf6d3cc464771e87ae4c5e2f45e9823278659d6f Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 28 Nov 2024 02:47:25 +0100 Subject: [PATCH 8/9] Add license to metadata --- src/ontology/taxrank-edit.obo | 1 + taxrank.obo | 1 + taxrank.owl | 7 +++++++ 3 files changed, 9 insertions(+) diff --git a/src/ontology/taxrank-edit.obo b/src/ontology/taxrank-edit.obo index 7c11b4a..caa523a 100644 --- a/src/ontology/taxrank-edit.obo +++ b/src/ontology/taxrank-edit.obo @@ -7,6 +7,7 @@ idspace: dcterms http://purl.org/dc/terms/ idspace: orcid https://orcid.org/ property_value: dcterms:contributor orcid:0000-0001-6512-3296 property_value: dcterms:contributor orcid:0000-0003-4423-4370 +property_value: dcterms:license https://creativecommons.org/publicdomain/zero/1.0/ [Term] id: TAXRANK:0000000 diff --git a/taxrank.obo b/taxrank.obo index 3f52f17..d50c3de 100644 --- a/taxrank.obo +++ b/taxrank.obo @@ -8,6 +8,7 @@ remark: To the extent possible under law, Peter E. Midford has waived all copyri ontology: taxrank property_value: dcterms:contributor orcid:0000-0001-6512-3296 property_value: dcterms:contributor orcid:0000-0003-4423-4370 +property_value: dcterms:license https://creativecommons.org/publicdomain/zero/1.0/ owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\n############################\n# Classes\n############################\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n\n) [Term] diff --git a/taxrank.owl b/taxrank.owl index 3b2963c..9f2d8e9 100644 --- a/taxrank.owl +++ b/taxrank.owl @@ -14,6 +14,7 @@ + taxonomic_rank 1.2 To the extent possible under law, Peter E. Midford has waived all copyright and related or neighboring rights to the Taxonomic Rank Vocabulary (TAXRANK). This work is published from the United States. It is requested that users of this vocabulary cite it at the following URI: http://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary @@ -68,6 +69,12 @@ + + + + + + From 00e7abd5e35880d799c514a1bc0d4de633da885b Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 28 Nov 2024 02:49:16 +0100 Subject: [PATCH 9/9] Add ontology root term --- src/ontology/taxrank-edit.obo | 7 +++++++ taxrank.obo | 7 +++++++ taxrank.owl | 12 ++++++++++++ 3 files changed, 26 insertions(+) diff --git a/src/ontology/taxrank-edit.obo b/src/ontology/taxrank-edit.obo index caa523a..82977c7 100644 --- a/src/ontology/taxrank-edit.obo +++ b/src/ontology/taxrank-edit.obo @@ -8,6 +8,7 @@ idspace: orcid https://orcid.org/ property_value: dcterms:contributor orcid:0000-0001-6512-3296 property_value: dcterms:contributor orcid:0000-0003-4423-4370 property_value: dcterms:license https://creativecommons.org/publicdomain/zero/1.0/ +property_value: IAO:0000700 TAXRANK:0000000 [Term] id: TAXRANK:0000000 @@ -557,3 +558,9 @@ id: IAO:0000112 name: example of usage is_metadata_tag: true namespace: iao + +[Typedef] +id: IAO:0000700 +name: has ontology root term +is_metadata_tag: true +namespace: iao diff --git a/taxrank.obo b/taxrank.obo index d50c3de..8e8ce9d 100644 --- a/taxrank.obo +++ b/taxrank.obo @@ -9,6 +9,7 @@ ontology: taxrank property_value: dcterms:contributor orcid:0000-0001-6512-3296 property_value: dcterms:contributor orcid:0000-0003-4423-4370 property_value: dcterms:license https://creativecommons.org/publicdomain/zero/1.0/ +property_value: IAO:0000700 TAXRANK:0000000 owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\n############################\n# Classes\n############################\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n\n) [Term] @@ -555,6 +556,12 @@ name: example of usage namespace: iao is_metadata_tag: true +[Typedef] +id: IAO:0000700 +name: has ontology root term +namespace: iao +is_metadata_tag: true + [Typedef] id: TAXRANK:1000000 name: has_rank diff --git a/taxrank.owl b/taxrank.owl index 9f2d8e9..2d3508e 100644 --- a/taxrank.owl +++ b/taxrank.owl @@ -12,6 +12,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + @@ -52,6 +53,17 @@ + + + + iao + IAO:0000700 + true + has ontology root term + + + +