omnisearch / omit Goto Github PK

What is the definition of "Length of Stay"? And what is the definition of Hospitalization? How can length of stay be a subclass to hospitalization?
We need "Length of Stay" to represent the period of time a hospitalization lasts (so it doesn't seem that is what you are representing).

Need to import this term from CHEBI

This property should change to BFO:has part imported from RO.
http://purl.obolibrary.org/obo/OBO_REL#_part_of

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

The URI is http://purl.obolibrary.org/obo/OMIT#SO_3000001. There is no class in SO with URI SO:3000001, although 'region' (SO:0000001) does have 'sequence' as an exact synonym.

There are a number of unsats in OMIT (2494), mostly I think due to the fact that miRNA is classified both as small_regulatory_ncRNA (which is is generically dependent continuant), and 'non-coding RNA', which is classified as a molecular entity. Is OMIT still maintained? Would you be able to fix this problem?

RO_0000085 (http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0000085)
RO_0002331 (http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002331)

Both of them appears URI only without other information.

Can "Amino Acids, Peptides, and Proteins" http://purl.obolibrary.org/obo/OMIT_0002019 be moved from its current "quality > MeSH Terms > Chemicals and Drug Category" path over to "molecular entity"? Most of the other "Chemicals and Drug Category" subclasses need to be moved too it seems?!

Need to import this term from IAO.

This is the BFO has part term.
I think it has changed to another URI, since BFO2 has part changed to accommodate the temporal relations.
It's better to import this term from RO. http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/BFO_0000051

all of the following are in OMIT but these are not in scope for an ontology of microRNAs

Example - the following should have NCBITaxon IDs not OMIT IDs:

The following all have OMIT IRIs, why is CHEBI not imported?

and so on

OMIT includes a class 'MeSH term' that is a subclass of quality:

It does not make sense to make these subclasses of quality, and it is unusual for an OBO ontology to duplicate all of MeSH

(1) Create a new OMIT class "MeSH_term" to replace the imported term "phenotype"

(2) As far as I can tell, the class "xsd_string" is not used at all. If this is the case, we can completely remove the imports.owl file - all classes in this file are already included in various xxx-imports.owl files from the ncro.owl, EXCEPT FOR "phenotype" and "xsd_string"

(3) Clean up the files at https://github.com/OmniSearch/omit/tree/master/src/ontology, following the ncro style:

• We only need: omit.owl, omit.obo, ncro.owl, catalog-v001.xml, and (optional) README.md,
• Move all other files to "Obsolete"
• Create a new folder "ontofox-inputs" for future use (eventually we will create ncro-imports.owl to replace ncro.owl, and will need ncro.txt in the "ontofox-inputs" folder)

The current purl redirect of omit ("http://soc.southalabama.edu/~huang/OMIT/Ontology/OMIT.owl") needs to be changed to: https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.owl