Update KG to comply with the emerging Translator KG spec

[saramsey]

Here is a proposed minimal integration:
https://docs.google.com/spreadsheets/d/1zXitcR1QjHyh6WocukgshSR7IoAVg7MJQG-HNh96Jec/edit#gid=3366698

Here is a proposed maximal integration:
https://docs.google.com/spreadsheets/d/1zXitcR1QjHyh6WocukgshSR7IoAVg7MJQG-HNh96Jec/edit#gid=421374962

[saramsey]

DO THIS WORK IN A BRANCH

[dkoslicki]

What would also be helpful is to have URL's/URI's/PURL's as node properties. Eg. our node "OMIM:603903" would have as a property (called URL/URI/whatever): "http://omim.org/entry/603903"

[dkoslicki]

See #19

[saramsey]

This has been requested by April 16

[saramsey]

planning to do this work in branch "newkg"

[saramsey]

I am working on issue # 34 (updating our KG to comply with the spec from Matthew Brush et al.). FYI, Neo4j doesn’t seem to allow a relationship type to have a space in it. And most of the predicates in the new spec have spaces in them. So I am mapping spaces to underscores, which are more neo4j-friendly.

If I am way off base in “interpreting” the spec in this way, please let me know.

[saramsey]

I wrote:

Eric & David,

What is the actual specification for the properties of the nodes in the KG? (I have the relationships under control, I think).

I need a list of name-value pairs, like this:

name = CURIE identifier of the bioentity
iri = IRI of the bioentity
description = human-readable description

Thanks,
Steve

Response from @edeutsch:

I don’t know that this has been hammered out. Maybe we can set the standard. In my proposed API example and definition I have this:

{ "@id": "https://www.uniprot.org/uniprot/P00738",
"@type": "Protein",
"name": "Haptoglobin",
"symbol": "HP",
"accession": "P00738",
"description": "Haptoglobin captures, and combines with free plasma hemoglobin...",
"node_attributes": [
{ "@type": "",
"name": "",
"value": "",
"url": "",
} ]

I think we should align these if possible.

In the KG merging document (one of them anyway) is this:

node properties:
· id
· name
· description
· identifiers:
o e.g. DOID, HGNC, Orphanet
· metadata (JSON string)

Maybe a good discussion topic for Monday is to decide how we should set the standard.

What would really help the discussion is some real live example for various node types (i.e. robust examples with copious properties, not bare bones ones)

Eric

[dkoslicki]

@saramsey Did you see the question regarding s/participates_in/participates_in/g? participates_in wasn't in the old KG, so I don't know if you meant a different substitution here...

[saramsey]

@dkoslicki the predicate "participates_in" is in the KG as of the completion of issue #13

see this version of BioNetExpander.py, lines 82 and 240: https://github.com/RTXteam/RTX/blob/master/code/reasoningtool/BioNetExpander.py

[saramsey]

Not sure if the pre-issue-34 but post-issue-13 KG ever got pushed to rtx.ncats.io, or even rtxdev. But it did exist on rtxsteve, as shown in this screen capture from an email I sent to you on 3/26:

[saramsey]

@dkoslicki Does that clarify things?

[dkoslicki]

@saramsey Yes, that makes sense. My code doesn't yet leverage GO (and it wasn't updated in rtx.ncats.io), so that's why I wasn't seeing it. So I think I'm good now

[saramsey]

s/is_parent_of/subset_of/g (with direction of edge reversed)

[dkoslicki]

@saramsey Got it! I'm about to do the refactoring, so let me know if anything about the following seems amiss. I'll wait to hit the button until I get confirmation (hard to go back after I do it):

s/\<uniprot_protein\>/protein/g
s/\<pharos_drug\>/chemical_substance/g
s/\<ncbigene_microrna\>/microRNA/g
s/\<reactome_pathway\>/pathway/g
s/\<anatont_anatomy\>/anatomical_entity/g
s/\<geneont_bioprocess\>/biological_process/g
s/\<phenont_phenotype\>/phenotypic_feature/g
s/\<omim_disease\>/disease/g
s/\<disont_disease\>/disease/g
s/\<disease_affects\>/affects/g
s/\<is_member_of\>/participates_in/g
s/\<gene_assoc_with\>/associated_with_condition/g
s/\<phenotype_assoc_with\>/has_phenotype/g
s/\<interacts_with\>/directly_interacts_with/g
s/\<controls_expression_of\>/regulates/g
s/\<is_expressed_in\>/expressed_in/g
s/\<targets\>/directly_interacts_with/g
s/\<controls_state_change_of\>/regulates/g
s/\<participates_in\>/participates_in/g
s/\<is_parent_of\>/subset_of/g
s|http://neo4j:precisionmedicine@rtx.ncats.io:7473/db/data|http://neo4j:precisionmedicine@rtxdev.saramsey.org:7674/db/data|g
s|bolt://rtx.ncats.io:7687|bolt://rtxdev.saramsey.org:7887|g

In particular, that's the right KG and bolt protocol, correct?

[dkoslicki]

@saramsey @edeutsch From my perspective, the newkg branch can be merged into master (as my QuestionAnswering code is running without error). Shall we merge and close this issue soon?

[saramsey]

done

…

----------------------------------------------------- Stephen Ramsey Assistant Professor, Oregon State University * School of Electrical Engineering and Computer Science * Department of Biomedical Sciences 208A Dryden Hall stephen.ramsey@oregonstate.edu<mailto:stephen.ramsey@oregonstate.edu> http://lab.saramsey.org On Apr 13, 2018, at 7:48 PM, David Koslicki <notifications@github.com<mailto:notifications@github.com>> wrote: @saramsey<https://github.com/saramsey> @edeutsch<https://github.com/edeutsch> From my perspective, the newkg branch can be merged into master (as my QuestionAnswering code is running without error). Shall we merge and close this issue soon? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#34 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AFTe-_ySriN0yBQBA_Tpe4JYQ7XTFArqks5toWOFgaJpZM4S73qk>.

[saramsey]

Team Orange has changed relationship properties to snake-case; updating the code now

[saramsey]

since description field is optional, marking this closed

see KG here:
http://rtxdev.saramsey.org:7674

[saramsey]

latest changes to KG schema, from Matt Brush at the May hackathon in DC:

associated with condition => gene associated with condition
causes or contributes to => contributes to
directly interacts with => physically interacts with
directly interacts with => regulates
enables => capable of
is capable of => capable of
enables (anatomy to cellular component) => has part
participates in => involved in (GO)
participates in => participates in (reactome)