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monarch-initiative / mapping-walker

walks mapping graphs running boomer
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PMID filter #3

Open cmungall opened 2 years ago

cmungall commented 2 years ago

should OxO really return PMIDs as mappings? maybe this is an upstream OBO problem. cc @matentzn

- [rough endoplasmic reticulum](http://purl.obolibrary.org/obo/PLANA_0007514) SiblingOf [](http://purl.obolibrary.org/obo/PMID_30143032)                0.09999999999999998
- [gamma neoblast](http://purl.obolibrary.org/obo/PLANA_0000039) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27013241)             0.09999999999999998
- [central nervous system](http://purl.obolibrary.org/obo/PLANA_0000103) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27013241)             0.09999999999999998
- [neuropil](http://purl.obolibrary.org/obo/PLANA_0000470) SiblingOf [](http://purl.obolibrary.org/obo/PMID_29291981)           0.09999999999999998
- [neoblast](http://purl.obolibrary.org/obo/PLANA_0000429) SiblingOf [](http://purl.obolibrary.org/obo/PMID_19174194)           0.09999999999999998
- [muscle cell](http://purl.obolibrary.org/obo/PLANA_0000101) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27063937)                0.09999999999999998
- [Neurons](http://purl.obolibrary.org/obo/UMLS_C0027882) EquivalentTo [Neurons](http://purl.obolibrary.org/obo/MeSH_D009474)   (most probable) 0.8
- [dopaminergic neuron](http://purl.obolibrary.org/obo/PLANA_0000482) SiblingOf [](http://purl.obolibrary.org/obo/PMID_23903188)                0.09999999999999998
- [pharynx](http://purl.obolibrary.org/obo/PLANA_0000016) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27163480)            0.09999999999999998
- [clonogenic neoblast](http://purl.obolibrary.org/obo/PLANA_0000046) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27150006)                0.09999999999999998
- [GABAergic neuron](http://purl.obolibrary.org/obo/PLANA_0000464) SiblingOf [](http://purl.obolibrary.org/obo/PMID_29291981)           0.09999999999999998
- [neuron](http://purl.obolibrary.org/obo/PLANA_0000099) SiblingOf [](http://purl.obolibrary.org/obo/PMID_24040508)             0.09999999999999998
- [renal system](http://purl.obolibrary.org/obo/PLANA_0000088) SiblingOf [](http://purl.obolibrary.org/obo/PMID_19048075)               0.09999999999999998
- [central nervous system](http://purl.obolibrary.org/obo/PLANA_0000103) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27063937)             0.09999999999999998
- [body wall musculature](http://purl.obolibrary.org/obo/PLANA_0000240) SiblingOf [](http://purl.obolibrary.org/obo/PMID_19174194)              0.09999999999999998
- [central nervous system](http://purl.obolibrary.org/obo/PLANA_0000103) EquivalentTo [](http://purl.obolibrary.org/obo/PMID_29291981)  (most probable) 0.8
- [vitelline gland](http://purl.obolibrary.org/obo/PLANA_0000231) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27163480)            0.09999999999999998
- [neuron](http://purl.obolibrary.org/obo/CL_0000540) EquivalentTo [](http://purl.obolibrary.org/obo/NCIT_C12623)       (most probable) 0.8
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matentzn commented 2 years ago

OxO is currently not a mapping browser - it is a browser for cross-references. I don't think it would be a priority for changing that on the OxO side, because there is deliberately no filtering: all ?x oio:hasDbXref ?y are shown, regardless of the prefix of the ?y.. Sorry about that. However, we should work with the ontologies in our are to use hasDbXref correctly. @srobb1 for example would certainly be open to change her xrefs if she was told which AP to use to link a publication to a term: https://github.com/information-artifact-ontology/ontology-metadata/issues/94

srobb1 commented 2 years ago

Yes!! I am totally onboard to change my xrefs to whatever is appropriate.