Source Best practices

[JMante1]

When a new component is uploaded best practices are required for how the ontology is used to attribute to a source. The prov ontology is currently in use for the spec and it has been suggested that "wasDerivedFrom" should be used. Can we clarify what terms should be used to reference:

• A part that was pulled from genbank (how do you link to a GenBank identifier like M11180.2)
• How do you reference a pubmed id?
• How do you reference an addgene record?
• How do you reference a doi?
• How do you reference an igem part - via the igem to sbol conversion or via the original url to igem?
• What if a url is given as source that does not seem to be a doi or igem?

[cjmyers]

For PubMed:
https://identifiers.org/pubmed:16333295

[cjmyers]

http://purl.obolibrary.org/obo/OBI_0001617

[jakebeal]

This issue should probably be resolved in tandem with SynBioDex/SBOL-specification#439

[Gonza10V]

I would like to re open this conversation. To my understanding ExternallyDefined is the way to point to external definitions in databases which cover partially what @JMante1 describes. What do we do with random URLs, should they be supported or valid? How can we tell if you are pointing to a valid IRI?
This could also be affected by ExternallyDefined objects constrained to be a feature like in SynBioDex/SBOL-specification#439

[jakebeal]

I would propose that the approaches here group into three general categories:

1. Pointers to records that are SBOL or a format that can be meaningfully converted into SBOL (e.g., FASTA, GenBank)
2. Pointers to non-convertible materials that have an identifiers.org URI
3. Pointers to non-convertible materials that do not have an identifiers.org URI

For case 1, I think we will have different approached depending on whether one is using SynBioHub or SEP054, but in both cases I think we can basically treat it as a TopLevel object that happens to be stored elsewhere (and possibly in another format).

For case 2 and 3, I think we just leave the wasDerivedFrom, using identifiers.org if applicable.

What is the problem that you need to solve right now? Maybe that can focus the discussion.