New terms, issue #1176

[apmody]

New terms from issue #1176

Calling make all in following error that needs to be resolved:

MANCHESTER PARSE ERROR the expression 'specimen and (is_specified_output_of some 'collecting specimen from organism') and ('derives from' some trachea)' at row 70, column 8 in table "src/ontology/templates/biobank-specimens.tsv" cannot be parsed: encountered unknown 'trachea'

[jamesaoverton]

So far so good.

1. Please use the UBERON "replacement" terms from this comment: Specimen terms request  #1176 (comment) When that's done, I'll update the UBERON imports to fix the parse error.

2. Please remove 'aspiration specimen collection' from the table. It's not a type of specimen, so we'll put it somewhere else.

[jamesaoverton]

Thanks. I'll take care of the next step.

It would have been better not to commit the deletion of biobank-specimens.owl. I'll rebuild it.

[jamesaoverton]

I updated the imports and made some changes to the table.

Please use Protege to add 'aspiration specimen collection' to src/ontology/obi-edit.owl.

There are still some problems to fix for the aspirate stuff.

[beckyjackson]

@apmody there are a bunch of changes to biobank-specimens.tsv that are making it difficult to see what's changed. Is there a reason quotes were added to the definition source field? Since these are TSVs, not CSVs, I don't think we need to enclose these in quotes.

Side note, there's also some trailing space on some of those values (e.g. "Chris Stoeckert, NCI BBRB "). This was probably there before, but maybe we should clean this up at some point? Maybe a different PR.

[jamesaoverton]

I'm pretty sure that I ran make sort and it added these quotes (because the fields contain commas).

[beckyjackson]

Do we want to keep them or should I clean that up?

[jamesaoverton]

I think it's right now, and will be stable going forward.

[beckyjackson]

The definitions need to be cleaned up a bit. I gave some examples on the first two, but mainly I think it would be good for these definitions to match the general pattern of this sheet:

A specimen that is collected with X from Y

Where X is the method of collection (e.g., swab) and Y is the anatomical area (e.g. cervix)

Also make sure all the definitions start with a capital "A".

I also think it would be good to have definition sources for them. See my comment about sources on line 70.

[beckyjackson]

@apmody please disregard the review, I will update the definitions. Thanks!

[beckyjackson]

After updating the definitions, I re-ran make sort and it removed those quotes. I think that should be fine going forward?