colleenXu
commented
1 year ago I know this post is long and kinda intimidating >.<. I think you've done a good job overall (great attention to detail!).
I'll summarize the feedback as:
- we most likely want to do a deeper dive into the data to write more specific operations @andrewsu. See the "But regarding operations" section below.
- If we're interested in only "supplement treats disease" edges, we could narrow our scope to only the combos that seem to be representing this info. there seems to be associations that aren't really related to supplements in this resource (example)
- however, this resource seems to have many of the same issues as semmeddb. So does the parser need a similar amount of effort to remove entities with novelty 0, handle retired IDs, get a publication count for filtering, etc?
- trying to troubleshoot the issues you're having querying BTE (first point of "Addressing the issues you raised")
- some minor adjustments to the yaml, giving feedback on small parts of the x-bte annotation
Addressing the issues you raised
1. I'm not sure why you're getting that error when testing locally. I can paste the cURL you provided into my terminal and BTE will execute without errors * Postman converts my queries to the cURL snippet below, which is a bit different from what you provided. Maybe try that format? * Maybe run `git pull` and `npm run pull` to see if BTE updates. If it does, then run `npm run compile` to make sure any changes are incorporated. * If you still have issues, please post to our lab's #ncats-translator channel so multiple people can look into what's going on... * potentially useful reminder: you can test a local file, but it'll need 3 slashes (like I'm using `file:///Users/colleenxu/Desktop/translator-api-registry/_temp_testing/suppkg.yaml`). And if you adjust your yaml and then want to test it, you'll want to save your yaml file, stop/quit BTE, run the `API_OVERRIDE=true npm run smartapi_sync` command again, and then start BTE again. BTE won't automatically pull in the changescURL from Postman
``` curl --location 'http://localhost:3000/v1/smartapi/suppkg/query' \ --header 'Content-Type: application/json' \ --data '{ "message": { "query_graph": { "nodes": { "n0": { "ids": ["UMLS:C0008780"] }, "n1": { "categories": ["biolink:NamedThing"] } }, "edges": { "e01": { "subject": "n0", "object": "n1" } } } } } ' ```Minor yaml suggestions
* add a sentence in the `info.description` of the API: about the publication / what suppKG has inside, with a link to the publication * change version to what the BioThings API version is. It looks like it might be `2021`? * tag the endpoints with the path `/association/` as `association`. Right now they're tagged as `interaction`. My understanding is that this tag on endpoints is to group endpoints by path * in the currently commented-out `testExamples`, I provide the IDs in the format that they would be when querying in TRAPI format. So they have the biolink-model prefix (specified in inputs.id and outputs.id).Feedback on the current operations
* the `parameter.fields` section needs to list / encompass all the fields in the response-mapping because that part of the query tells the BioThings API what fields you want in the response. * also I suggest adding more fields: `relation.conf` and `relation.sentence` seem useful. * in the response-mapping, `input_name` and `output_name` are special keywords that tell BTE that these aren't edge-attributes - their values should actually be used to replace the node names when SRI Node Normalizer doesn't provide a human-readable name for those node's IDs. They should match the inputs/outputs of the operation: * subject-object's response-mapping `object` should have `input_name: subject.name` * object-subject's response-mapping `subject` should have `input_name: object.name`But regarding the operations
EDIT: @andrewsu and I have decided that this is a good next step.
With this resource, I think we'll need to write more specific operations, based on the set of unique combos of subject.semtypes,predicate,object.semtypes values (meta-triples). This probably involves analyzing the data underlying this API.
- counts and example triples would be nice
- It may also help to get a sense of how many subjects and objects have multiple values in semtypes vs just 1 value. For the operations, we'd want to set one of the semtypes fields, and I'm not sure if providing 1 value will do vs multiple values (using AND or OR?)
- The stuff I wrote in the summary at the top of this comment is still relevant (on narrower scope + semmeddb issues). We likely only want information on supplements.
Then, depending on how many unique combos there are, we could then decide whether we want to map to biolink-model / write operations manually or through code (like what we do with semmeddb).
Here's an example of what I think the format for operations would be (I've worked through it and tested it):
the x-bte operations and response-mapping section
``` SmallMolecule-treats-Disease: ## 595,222 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: - id: UMLS semantic: SmallMolecule requestBodyType: object requestBody: body: >- {"q": {{ queryInputs | replPrefix('predicate:TREATS AND object.semtypes:((dsyn) OR (neop)) AND subject.umls')| dump }}, "scopes": []} outputs: - id: UMLS semantic: Disease parameters: fields: object.umls,relation,subject.name,object.name size: 1000 predicate: treats source: "infores:suppkg" # no infores for suppkg yet response_mapping: "$ref": "#/components/x-bte-response-mapping/object" # testExamples: # - qInput: "UMLS:C0062737" ## histaglobin # oneOutput: "UMLS:C0002103" ## allergic rhinitis SmallMolecule-treats-Disease-rev: - supportBatch: true useTemplating: true inputs: - id: UMLS semantic: Disease requestBodyType: object requestBody: body: >- {"q": {{ queryInputs | replPrefix('predicate:TREATS AND subject.semtypes:((phsu) OR (orch)) AND object.umls')| dump }}, "scopes": []} outputs: - id: UMLS semantic: SmallMolecule parameters: fields: subject.umls,relation,subject.name,object.name size: 1000 predicate: treated_by source: "infores:suppkg" # no infores for suppkg yet response_mapping: "$ref": "#/components/x-bte-response-mapping/subject" # testExamples: # - qInput: "UMLS:C0263338" ## urticaria, chronic # oneOutput: "UMLS:C0062737" ## histaglobin x-bte-response-mapping: object: UMLS: object.umls suppkg_confidence_score: relation.conf ## not sure what to name this...you may know better? pubmed: relation.pmid "biolink:supporting_text": relation.sentence input_name: subject.name output_name: object.name subject: UMLS: subject.umls suppkg_confidence_score: relation.conf ## not sure what to name this...you may know better? pubmed: relation.pmid "biolink:supporting_text": relation.sentence input_name: object.name output_name: subject.name ```Example response from testing: suppkg.txt
notes:
- the q using OR is optional, and something I haven't used in x-bte annotations anywhere yet
- I changed the examples because the "adrenal cortex hormones" UMLS ID expands to >1000 IDs, so BTE won't actually execute the hop.
mnarayan1
andrewsu
YAML for the SuppKG API. The API is located here.
Notes:
NamedThingfor thesemanticfield of thex-bte-operationssection. Is there something more specific I should use instead?I've been trying to test my yaml file with this query:
Here is my
smartapi_overrides.jsonfile:However, I'm getting this error:
{"error":"Your input query graph is invalid","more_info":"Your Input Query Graph is invalid."}Are there any issues with my annotations? Should I format my query differently?