Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

What should Node descriptions look like? #374

Open
edeutsch opened this issue Sep 21, 2022 · 1 comment
Open

What should Node descriptions look like? #374

edeutsch opened this issue Sep 21, 2022 · 1 comment
Milestone

Comments

@edeutsch
Copy link
Collaborator

Can we standardize how we present descriptions in TRAPI?

ARAX:

            {
              "attribute_type_id": "biolink:description",
              "value": "A glycosidase that hydrolyzes a glucosylceramide to yield free ceramide plus glucose. Deficiency of this enzyme leads to abnormally high concentrations of glucosylceramide in the brain in GAUCHER DISEASE. EC 3.2.1.45.; UMLS Semantic Type: STY:T126; UMLS Semantic Type: STY:T116",
              "value_type_id": "metatype:String",
            },

Aragorn:

            {
              "attribute_type_id": "biolink:description",
              "value": "A class of organic compounds that contain nitrogen as the pivotal atom for functional groups. There are several different types of amines and the class is extensive.; UMLS Semantic Type: STY:T109",
              "value_type_id": "metatype:String",
            },

Explanatory:

            {
              "attribute_type_id": "biolink:description",
              "value": "A term used to describe a chemical structure of a compound containing a large lactone ring, usually with a 14 or 16-membered ring structure. The prototypical compounds within the macrolide class are the erythromycin-based antibiotics; however, many compounds with this chemical structure are being developed for other diseases.; A group of often glycosylated macrocyclic compounds formed by chain extension of multiple PROPIONATES cyclized into a large (typically 12, 14, or 16)-membered lactone. Macrolides belong to the POLYKETIDES class of natural products, and many members exhibit ANTIBIOTIC properties.; UMLS Semantic Type: STY:T121; UMLS Semantic Type: STY:T109",
              "value_type_id": "metatype:String"
            },

Improving? Not providing this that I can see
MolePro? Not providing that I can see
BTE? Not providing that I can see

So after a brief check, it seems that everyone that I could find some sort of result for and that is actually providing some descriptions is doing it the same way (perhaps only because they're getting this info passed from RTX-KG2?) or not providing it.

Is that a de facto standard?

@vdancik vdancik added this to the v1.4 milestone Feb 1, 2023
@Genomewide
Copy link

(IMO) It is worth considering this as related to or adjacent to a larger architecture topic around microservices. Currently, microservices have been stood up to address the UI needs for consistency of descriptions. From the UI perspective, it is worth considering the best description by node category and having that be consistent across all nodes that share that category.

From the architecture viewpoint, this is impacted by the philosophy of how we will handle microservices. This kind of data requirement would lessen the need for microservices that add potential points of failure.

What would the architecture group like to do long term? 1. continue to use microservices, 2. ways for the UI to host data, or 3. standardize and add information to nodes across Translator. Other?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants