make data available outside paywall

[mellybelly]

We need to make the recommendation that whatever minimum phenotype standard we implement, that it is referencable within the JATS standard for journals so that it can be made available outside the paywall.

http://jats.nlm.nih.gov/

[mellybelly]

I don't know why this one is closed, but this needs to be extremely well documented before the manuscript is published for journals to easily adopt. @cmungall @julesjacobsen @DoctorBud can you advise? Do we need to recommend JATS changes or is the new data tag sufficient? In either case, we should have examples in our documentation. see http://www.ncbi.nlm.nih.gov/books/NBK280240/

[cmungall]

It's open, the linked ticket is closed.

I don't really understand the ticket. Are we talking about extending JATS to directly represent phenotypes? Or something involving the JATS linking mechanism?

The first seems like a bad idea and out of scope for JATS? Perhaps the idea is to insert a super-minimal payload, e.g. a list of terms?

For the latter, I think this is more about the resource providing the phenopacket rather than the standard itself. If the phenopacket is in FigShare, you'd follow the example for data in figshare. Maybe I'm misunderstanding...

[mellybelly]

Well, I think that the easiest thing to do is to use the JATS data citation extension as it is now, your minimal payload option, that resolves to a DOI or other persistent ID where the phenopacket lives. The question is do we need another extension or tag, to indicate that it is a phenopacket as a special type of dataset? or perhaps this does not matter. But, we should think about all the contexts where not having any typing might matter:

• querying a journal API and not having to iterate through all the linked datasets
• displaying phenopackets in Pubmed
• a journal querying other pubs for similar phenopackets

regardless we need examples that show how this works. I'll try to talk to the JATS folks for advice, perhaps @jmcmurry can too