Update fp-002-format.md

[nataled]

Revised to conform to new standard format.

[cthoyt]

what about OBO Graph JSON?

[nataled]

(Just an FYI: The text above was pulled from existing text found within the criteria for review link for this principle.)

I don't know enough about that format. I would say that any format convertible by ROBOT or Protege is fair game. Is that the case for OBO Graph JSON? If so, I'll generalize the statement and add that as another example.

[cthoyt]

Yes, ROBOT also will generate OBO Graph JSON. I think you're right that it's good to mention that any other exports will probably help people

[jamesaoverton]

My suggestion would be to replace the first sentence of this paragraph with: "Ontologies can OPTIONALLY produce products in other formats. For historical reasons, OBO-Format files are often produced." Then the rest of the paragraph (as written) is an example of a .obo product.

[cthoyt]

Recommendations on validating OBO file format if curation is done primarily there?

[nataled]

There is an ongoing discussion about whether or not the Foundry will take up the task of converting file formats. If the answer is 'yes', then we'd indeed need to say something about validating OBO format (and OBO Graph JSON and Manchester and others). Perhaps it would be enough to recommend that the developers at least attempt to use their file as input for ROBOT or Protege, both of which would complain if the format is incorrect.

[cthoyt]

For parsing OBO, there is also @althonos's pronto package. I'd recommend it with the caveat that it's quite strict and curators don't tend to like being told they've made mistakes by a computer program

[althonos]

For the purpose of validation, i also wrote fastobo-validator that is available in the ODK, it's a bit better at reporting errors (and can detect some additional issues pronto can't find, like frames with duplicate definitions or broken ISBN references).

[matentzn]

All the curators I know love to be told they made a mistake by a computer program.. In fact, many of them love to code nowadays!

[matentzn]

@nataled I don't think we should take on any such responsibilities (transformations into OBO etc) - we need to decentralise and enable (fishing rod) through tools and training rather than providing services that maintain the technical illiteracy. I would just add a link to fast-obo validator here as a way for people to validate their OBO formats (90% of all OBO files use ROBOTs ominous --check false which means they are broken). As EWG you need to decide wether we would want to require non-broken OBO as part of dashboard checking - I think that's a huge churn, but possible useful. No idea whats best.

[cthoyt]

@matentzn you're lucky to know such good curators! I am thinking back to the dark days of my PhD where I became a heretic when introducing the PyBEL biological expression language validator.

I agree with @matentzn - centralizing working with the data itself wouldn't be sustainable. Reporting on what could be converted might be a useful metric, but I wouldn't say it should be required at the moment

[nataled]

@matentzn @cthoyt the decision to provide or not provide conversion services is not one the EWG makes. ALL principles decisions are made by Ops; EWG just puts them into words. The wording reflected above is merely a rewrite of what's already given in the principle and in the FAQ (IIRC). As I mentioned in my previous comment, there is an unfinished discussion about what services the Foundry are willing to provide in this regard. It's been proposed that we do NOT provide the conversion service, and so far as I recall, that seems to be the way it will be, but, again, until it is finalized the EWG cannot take the sentence out.

[jamesaoverton]

I don't see the need to mention OBO-format validators on the Principle page. In general, there's so much to know about ontology development best practises, and that sort of documentation should live somewhere else.

[matentzn]

I am happy with the content, @nataled if you want to add anything minor I am still fine, but I am happy for this to go.

[jamesaoverton]

Sorry to be slow to look at this.

Regarding "the OBO central build pipeline will do this for you", my understanding is that this service is no longer provided, and so this part of the Principle need to be changed. More details in #1446.