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Add proper mappings management #2361

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merged 9 commits into from
Apr 27, 2024
Merged

Add proper mappings management #2361

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e0c7321
Declare the mapping sets to the ODK.
gouttegd Apr 19, 2024
f07cff2
Commit re-generated Makefile.
gouttegd Apr 25, 2024
9bbcb69
Add custom rules to generate the mapping sets.
gouttegd Apr 25, 2024
51f9851
Use SSSOM/T-OWL to create the mappings.owl component.
gouttegd Apr 25, 2024
c248bd9
Remove the FBbt mapping set from src/ontology/mappings.
gouttegd Apr 26, 2024
97bbc8f
Ignore the locally generated SSSOM files.
gouttegd Apr 26, 2024
fce59a6
Set proper mapping set IDs when extracting cross-references.
gouttegd Apr 26, 2024
8492695
Publish the meta mapping set.
gouttegd Apr 26, 2024
e72632b
Commit external mapping set files.
gouttegd Apr 26, 2024
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,8 @@ src/ontology/subsets/BDS_subset.tsv
src/ontology/subsets/BDS_subset.owl
src/ontology/subsets/BDS_subset.obo
src/ontology/subsets/BDS_subset.json
src/mappings/cl-local.sssom.tsv
src/mappings/cl.sssom.tsv
cl.json
cl.owl
cl-simple.owl
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6 changes: 6 additions & 0 deletions src/mappings/README.md
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@@ -0,0 +1,6 @@
# SSSOM mapping directory

Do not overwrite, contents will be generated automatically.



98 changes: 98 additions & 0 deletions src/mappings/fbbt.sssom.tsv
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#curie_map:
# CL: "http://purl.obolibrary.org/obo/CL_"
# FBbt: "http://purl.obolibrary.org/obo/FBbt_"
# ORCID: "https://orcid.org/"
# obo: "http://purl.obolibrary.org/obo/"
#mapping_set_id: "http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv"
#mapping_set_description: "Mappings between the Drosophila Anatomy Ontology and foreign ontologies."
#creator_id:
# - "ORCID:0000-0002-6095-8718"
#license: "https://creativecommons.org/licenses/by/4.0/"
#subject_source: "obo:fbbt.owl"
#object_source: "obo:cl.owl"
#mapping_date: "2024-04-24"
subject_id subject_label predicate_id object_id mapping_justification
FBbt:00000092 primordial germ cell semapv:crossSpeciesExactMatch CL:0000301 semapv:ManualMappingCuration
FBbt:00000124 epithelial cell semapv:crossSpeciesExactMatch CL:0000066 semapv:ManualMappingCuration
FBbt:00001666 cardioblast semapv:crossSpeciesExactMatch CL:0000465 semapv:ManualMappingCuration
FBbt:00001685 embryonic/larval plasmatocyte semapv:crossSpeciesExactMatch CL:0000394 semapv:ManualMappingCuration
FBbt:00001687 lamellocyte semapv:crossSpeciesExactMatch CL:0000396 semapv:ManualMappingCuration
FBbt:00001689 procrystal cell semapv:crossSpeciesExactMatch CL:0000395 semapv:ManualMappingCuration
FBbt:00001690 embryonic/larval crystal cell semapv:crossSpeciesExactMatch CL:0000715 semapv:ManualMappingCuration
FBbt:00001691 polygonal cell semapv:crossSpeciesExactMatch CL:0000398 semapv:ManualMappingCuration
FBbt:00001789 histoblast semapv:crossSpeciesExactMatch CL:0000373 semapv:ManualMappingCuration
FBbt:00003219 adepithelial cell semapv:crossSpeciesExactMatch CL:0000462 semapv:ManualMappingCuration
FBbt:00003360 flight muscle cell semapv:crossSpeciesExactMatch CL:0000196 semapv:ManualMappingCuration
FBbt:00003686 Kenyon cell semapv:crossSpeciesExactMatch CL:0000673 semapv:ManualMappingCuration
FBbt:00004101 peptidergic neuron semapv:crossSpeciesExactMatch CL:0000110 semapv:ManualMappingCuration
FBbt:00004193 cone cell semapv:crossSpeciesExactMatch CL:0000718 semapv:ManualMappingCuration
FBbt:00004211 photoreceptor cell semapv:crossSpeciesExactMatch CL:0000210 semapv:ManualMappingCuration
FBbt:00004213 photoreceptor cell R1 semapv:crossSpeciesExactMatch CL:0000687 semapv:ManualMappingCuration
FBbt:00004215 photoreceptor cell R2 semapv:crossSpeciesExactMatch CL:0000690 semapv:ManualMappingCuration
FBbt:00004217 photoreceptor cell R3 semapv:crossSpeciesExactMatch CL:0000694 semapv:ManualMappingCuration
FBbt:00004219 photoreceptor cell R4 semapv:crossSpeciesExactMatch CL:0000697 semapv:ManualMappingCuration
FBbt:00004221 photoreceptor cell R5 semapv:crossSpeciesExactMatch CL:0000702 semapv:ManualMappingCuration
FBbt:00004223 photoreceptor cell R6 semapv:crossSpeciesExactMatch CL:0000705 semapv:ManualMappingCuration
FBbt:00004225 photoreceptor cell R7 semapv:crossSpeciesExactMatch CL:0000707 semapv:ManualMappingCuration
FBbt:00004227 photoreceptor cell R8 semapv:crossSpeciesExactMatch CL:0000709 semapv:ManualMappingCuration
FBbt:00004230 pigment cell semapv:crossSpeciesExactMatch CL:0001658 semapv:ManualMappingCuration
FBbt:00004861 germline stem cell semapv:crossSpeciesExactMatch CL:0000014 semapv:ManualMappingCuration
FBbt:00004873 female germline stem cell semapv:crossSpeciesExactMatch CL:0000022 semapv:ManualMappingCuration
FBbt:00004878 nurse cell semapv:crossSpeciesExactMatch CL:0000026 semapv:ManualMappingCuration
FBbt:00004886 oocyte semapv:crossSpeciesExactMatch CL:0000023 semapv:ManualMappingCuration
FBbt:00004903 follicle stem cell semapv:crossSpeciesExactMatch CL:0000441 semapv:ManualMappingCuration
FBbt:00004904 follicle cell semapv:crossSpeciesExactMatch CL:0000477 semapv:ManualMappingCuration
FBbt:00004905 border follicle cell semapv:crossSpeciesExactMatch CL:0000579 semapv:ManualMappingCuration
FBbt:00004906 centripetal follicle cell semapv:crossSpeciesExactMatch CL:0000671 semapv:ManualMappingCuration
FBbt:00004910 stalk follicle cell semapv:crossSpeciesExactMatch CL:0000674 semapv:ManualMappingCuration
FBbt:00004929 male germline stem cell semapv:crossSpeciesExactMatch CL:0000016 semapv:ManualMappingCuration
FBbt:00004934 primary gonial cell semapv:crossSpeciesExactMatch CL:0000020 semapv:ManualMappingCuration
FBbt:00004935 spermatogonium semapv:crossSpeciesExactMatch CL:0000020 semapv:ManualMappingCuration
FBbt:00004936 spermatocyte semapv:crossSpeciesExactMatch CL:0000017 semapv:ManualMappingCuration
FBbt:00004941 secondary spermatocyte semapv:crossSpeciesExactMatch CL:0000657 semapv:ManualMappingCuration
FBbt:00004942 spermatid semapv:crossSpeciesExactMatch CL:0000018 semapv:ManualMappingCuration
FBbt:00004954 spermatozoon semapv:crossSpeciesExactMatch CL:0000019 semapv:ManualMappingCuration
FBbt:00004994 epidermoblast semapv:crossSpeciesExactMatch CL:0000464 semapv:ManualMappingCuration
FBbt:00004995 oenocyte semapv:crossSpeciesExactMatch CL:0000487 semapv:ManualMappingCuration
FBbt:00005038 tracheocyte semapv:crossSpeciesExactMatch CL:0008026 semapv:ManualMappingCuration
FBbt:00005058 pericardial cell semapv:crossSpeciesExactMatch CL:0000474 semapv:ManualMappingCuration
FBbt:00005059 garland cell semapv:crossSpeciesExactMatch CL:0000486 semapv:ManualMappingCuration
FBbt:00005062 prohemocyte semapv:crossSpeciesExactMatch CL:0000385 semapv:ManualMappingCuration
FBbt:00005063 hemocyte semapv:crossSpeciesExactMatch CL:0000387 semapv:ManualMappingCuration
FBbt:00005070 visceral muscle cell semapv:crossSpeciesExactMatch CL:0008007 semapv:ManualMappingCuration
FBbt:00005073 somatic muscle cell semapv:crossSpeciesExactMatch CL:0008004 semapv:ManualMappingCuration
FBbt:00005074 muscle cell semapv:crossSpeciesExactMatch CL:0000187 semapv:ManualMappingCuration
FBbt:00005083 myoblast semapv:crossSpeciesExactMatch CL:0000056 semapv:ManualMappingCuration
FBbt:00005106 neuron semapv:crossSpeciesExactMatch CL:0000540 semapv:ManualMappingCuration
FBbt:00005123 motor neuron semapv:crossSpeciesExactMatch CL:0000100 semapv:ManualMappingCuration
FBbt:00005124 sensory neuron semapv:crossSpeciesExactMatch CL:0000101 semapv:ManualMappingCuration
FBbt:00005125 interneuron semapv:crossSpeciesExactMatch CL:0000099 semapv:ManualMappingCuration
FBbt:00005128 pioneer neuron semapv:crossSpeciesExactMatch CL:0000116 semapv:ManualMappingCuration
FBbt:00005130 neurosecretory neuron semapv:crossSpeciesExactMatch CL:0000165 semapv:ManualMappingCuration
FBbt:00005131 dopaminergic neuron semapv:crossSpeciesExactMatch CL:0000700 semapv:ManualMappingCuration
FBbt:00005133 serotonergic neuron semapv:crossSpeciesExactMatch CL:0000850 semapv:ManualMappingCuration
FBbt:00005144 glial cell semapv:crossSpeciesExactMatch CL:0000125 semapv:ManualMappingCuration
FBbt:00005145 glioblast semapv:crossSpeciesExactMatch CL:0000340 semapv:ManualMappingCuration
FBbt:00005146 neuroblast semapv:crossSpeciesExactMatch CL:0000338 semapv:ManualMappingCuration
FBbt:00005147 neuroglioblast semapv:crossSpeciesExactMatch CL:0000468 semapv:ManualMappingCuration
FBbt:00005149 ganglion mother cell semapv:crossSpeciesExactMatch CL:0000469 semapv:ManualMappingCuration
FBbt:00005169 trichogen cell semapv:crossSpeciesExactMatch CL:0000374 semapv:ManualMappingCuration
FBbt:00005171 tormogen cell semapv:crossSpeciesExactMatch CL:0000372 semapv:ManualMappingCuration
FBbt:00005173 thecogen cell semapv:crossSpeciesExactMatch CL:0000380 semapv:ManualMappingCuration
FBbt:00005219 scolopale cell semapv:crossSpeciesExactMatch CL:0000382 semapv:ManualMappingCuration
FBbt:00005221 scolopidial ligament cell semapv:crossSpeciesExactMatch CL:0000407 semapv:ManualMappingCuration
FBbt:00005412 gamete semapv:crossSpeciesExactMatch CL:0000300 semapv:ManualMappingCuration
FBbt:00005797 Malpighian tubule Type II cell semapv:crossSpeciesExactMatch CL:1000155 semapv:ManualMappingCuration
FBbt:00005812 myotube semapv:crossSpeciesExactMatch CL:0002372 semapv:ManualMappingCuration
FBbt:00005917 lymph gland derived hemocyte semapv:crossSpeciesExactMatch CL:0000735 semapv:ManualMappingCuration
FBbt:00006009 eye photoreceptor cell semapv:crossSpeciesExactMatch CL:2000019 semapv:ManualMappingCuration
FBbt:00007002 cell semapv:crossSpeciesExactMatch CL:0000000 semapv:ManualMappingCuration
FBbt:00007108 imaginal disc epithelial cell semapv:crossSpeciesExactMatch CL:0000429 semapv:ManualMappingCuration
FBbt:00007173 cholinergic neuron semapv:crossSpeciesExactMatch CL:0000108 semapv:ManualMappingCuration
FBbt:00007228 GABAergic neuron semapv:crossSpeciesExactMatch CL:0000617 semapv:ManualMappingCuration
FBbt:00007325 epidermal cell semapv:crossSpeciesExactMatch CL:0000463 semapv:ManualMappingCuration
FBbt:00007367 histaminergic neuron semapv:crossSpeciesExactMatch CL:0011110 semapv:ManualMappingCuration
FBbt:00048032 glycinergic neuron semapv:crossSpeciesExactMatch CL:1001509 semapv:ManualMappingCuration
FBbt:00057012 female germline cell semapv:crossSpeciesExactMatch CL:0000025 semapv:ManualMappingCuration
FBbt:00058020 juvenile hormone secreting cell semapv:crossSpeciesExactMatch CL:0000482 semapv:ManualMappingCuration
FBbt:00100291 glutamatergic neuron semapv:crossSpeciesExactMatch CL:0000679 semapv:ManualMappingCuration
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