tutorial on phenoscape API's

[snacktavish]

@blubbundbla and I have been working through https://phenoscapekb.docs.apiary.io, but we have some questions! a tutorial on the phenoscape API's would be great.

[balhoff]

Oh no! I forgot to update the link on the front page to http://kb.phenoscape.org/apidocs/

It is more complete. You will probably still have many questions.

[sckott]

@balhoff some thoughts/questions

• would it be possible to give back application/json when returning an error instead of text/plain?
• I'm not super familiar with Phenoscape yet - wondering if it'd be possible to give eg values for parameters in the swagger docs, so one can quickly get a sense for response structure
• pagination: do we assume that all results are returned on any request? i don't see any info on pagination, so i assume that's the case (UPDATE: now i see pagination for some routes, e.g, /study/phenotypes)
• looks like only GET requests allowed. seems like other methods aren't rejected though, maybe that's by design?: e.g.,

curl -v -XPOST http://kb.phenoscape.org/api/term/search?text=femur

*   Trying 152.3.104.142...
* TCP_NODELAY set
* Connected to kb.phenoscape.org (152.3.104.142) port 80 (#0)
> POST /api/term/search?text=femur HTTP/1.1
> Host: kb.phenoscape.org
> User-Agent: curl/7.54.0
> Accept: */*

< HTTP/1.1 200 OK
... 

[zhilianghu]

I am interested to learn what/how Phenoscape does.

Also I am interested to explore web tools that

• are handy and easy to deploy for ontology hierarchies display (we are using AmiGO 1.x; look for easy to use alternatives);

• interactively allow user to play the hierarchy displays (cytoscape-like);

• I have a use case where we try to manage trait data with multiple modifiers. For example, cow "milk yields" measures for her first 305 days (time as modifier) from her first parity (parity as modifier), and so on. I currently call it trait "variants" as a first parity 305 days milk yield cannot be a child of its own, conceptually. I am interest to learn how others handle this.

-- Zhiliang

[balhoff]

@sckott

would it be possible to give back application/json when returning an error instead of text/plain?

Probably so! This isn't something I've spent much time on so right now it's just a default result.

I'm not super familiar with Phenoscape yet - wondering if it'd be possible to give eg values for parameters in the swagger docs, so one can quickly get a sense for response structure

Definitely—I think there are a few but it can be expanded.

pagination: do we assume that all results are returned on any request? i don't see any info on pagination, so i assume that's the case (UPDATE: now i see pagination for some routes, e.g, /study/phenotypes)

Yep, many of the services have limit and offset parameters. Maybe it would be more intuitive to collapse that to page. But if you set limit to 0 you will generally get all the results.

looks like only GET requests allowed. seems like other methods aren't rejected though, maybe that's by design?: e.g.,

Most are intended to be used with GET, but as you say other methods aren't rejected. Perhaps that should be tightened up.

[sckott]

Thanks @balhoff - just some things that came to mind off the top. I'll stop here as I don't want to derail @snacktavish issue :/