mapping-commons/lmha-obo-mappings

very drafy first pass

lmha-obo-mappings's Issues

use lmha to gapfill cl uberon

using https://github.com/mapping-commons/lmha-obo-mappings/blob/main/mappings/lmha-nomatches.sssom.tsv

Map other lungmap ontologies

So I am a bit confused by the different lungmap ontologies. My initial alignment was on the webprotege file from the link Bruce provided

but on the lungmap site there are different OWL files https://lungmap.net/resources/ontologies/

• Human Alveolar Stage - PDF | Word | OWL
• Cell Ontology for Human Lung Maturation - PDF | Word | OWL
• Mouse Canalicular (E16.5-E17.5), Prenatal (early-mid) Saccular (E17.5-E19.5), Postnatal (mid-late) Saccular (P0-P03), Alveolar (P04-P36) Stages - PDF | Word | OWL
• Cell Ontology for Mouse Lung Maturation - PDF | Word | OWL

I think the first is identical to what Bruce provided

looking at the first two, confusingly they have the same ontology ID

$ grep '<owl:Ontology' ~/Downloads/LMHA_20190512*owl
/Users/cjm/Downloads/LMHA_20190512.owl:    <owl:Ontology rdf:about="http://www.lungmap.net/ontologies/human_anatomy">
/Users/cjm/Downloads/LMHA_20190512_Cell.owl:    <owl:Ontology rdf:about="http://www.lungmap.net/ontologies/human_anatomy">

however, they have different but highly overlapping content

• the _Cell file seems to be largely a subset of the other file, just the cell types
• however, there is some additional classification

telocyte in the cells file:

telocyte in the broader file:

the second file drops the "connective tissue cell" and adds all the incorrect part-ofs