General refactoring of Tools & APIs

[lpalbou]

We have an increased number of tools (GO Ribbon, GO-CAM widget, GO Matrix) and APIs (REST, SPARQL, GOLr) and the website could do a better job at listing them.

Proposals

• properly differentiate APIs (services to query data) from Tools (high-level UI to accomplish a function)
• in that spirit, rename the markdown page "tool-guide" in "api-guide" to avoid anymore confusion
• create a top-level menu either "Tools & APIs" or "Services" to list them and give quick access
• ensure each Tool & API is properly listed and documented from the menu and the bottom right card on the main page
• for API, ideally provide hands-on (e.g. Jupyter notebooks)

Note

The refactoring of the website should be done once the GO API is refactored, to avoid advertising and teaching users on things that are gonna be deprecated.

[suzialeksander]

In the meantime, I'm not sure all the links are going to the right places:
https://geneontology.github.io/docs/tools-guide/#query-go-ontology-and-annotations-with-biolink

The GO BioLink API implementation and its associated swagger documentation are available at http://api.geneontology.org/api

But http://api.geneontology.org/api sends me to a nearly blank page that only says "No API definition provided." If I backtrack to https://api.geneontology.org/ there's a link to
Swagger UI:http://localhost:8888/api

@lpalbou could you double check these? Or should I at least remove them temporarily if we're going to go ahead and redo this page?

[lpalbou]

Hi suzi:

1. yes all the links are correct.

2. for the GO API, I am pretty sure you were trying to access httpS://api.geneontology.org/api and not http://api.geneontology.org/api as it's still working :

I double check and the link on the tool page does redirect to the correct http://api.geneontology.org/api . Long story short, the swagger UI doesn't work in httpS as there was an issue in the Flask/REST library at the time. There is also no easy way to alter the httpS page as this is generated on the fly by Flask/REST.

However, as part of the general refactoring of API, this shouldn't matter as we would have a brand new API.