OpenWetWare: Where DOI Begin(s)?

MediaWiki is the software that is built on. We customize it by applying out own styling to the page, add out own member management software to it, and either write our own extensions to it or download and install others. In general, we try like hell to not touch the ‘core’ MediaWiki code. It would be like a lab scientist starting with a standard protocol and then making many modifications to it for his or her own purpose. That’s OK until someone makes a set of modifications to the protocol you started with. You now have to figure out how to retrofit your procedures, ingredients, and what-not with the new ones. Sometimes it’s easy. But sometimes it’s just too much and you revert back to the original, throwing out your own potentially useful enhancements.

MediaWiki has a number of built-in features. One of them is the “magic link” feature I mentioned in the last message. For some reason, someone added a feature to MediaWiki that, when a specific keyword was found, it would try to see if the next word was recognizable and do something on that basis. In the case I discussed, it was the “PMID” word followed by a recognizable PubMed number. The rules for such a number are very simple to understand. But they are not always easy to make work reliably. Since any series of numbers will be seen as a PMID, the wiki page will now contain a link to the PubMed database, offering users the chance to see the citation for a paper. If the paper doesn’t exist, the lookup will still take place. As the saying goes, “Garbage in, garbage out”. The change we made was a bit of a “core” change, but we’ve already moved it into an ‘extension’, thus allowing us to move to a new MediaWiki version without losing our ‘core-like’ change.

We removed another built-in document identifier that was built into MediaWiki. This one was ‘RFC’. The term came from the Internet. All aspects of Internet standards are documented in a “Request For Comment”. Biopart RFC standards are based upon similar documents and processes. In this case, we removed the RFC “magic links” to keep OpenWetWare for turning references to Biopart RFC’s into Internet RFC’s.

MediaWiki also supports magic links for ISBN number lookup as well. Again, the very simple syntax of the number itself makes this possible.

One identifier that’s conspicuously absent from this list of global standards is the academic publishing world’s standard, the DOI.The Document Object Indetifier. The standard has a is different from some of the other schemes. For one thing, you need to pay to obtain a license to issue them. Another is that you also, as far as we have ever determined, need to pay for each DOI issued. Unlike the simple, regular nature of the PMID, the DOI label itself is a variable string that isn’t easy to handle. Once you have located a DOI in a document, to resolve the publication it came from, a third-party needs to step in to do the actual lookup.

In the US, the PubMed database is administered by the NIH. Any PMID can be looked up via a single interface. The simplicity of this is what allowed Pubget to step in and cut out the NIH by directing a reader with a valid subscription to the actual text of a PMID-identified reference.

You can do something of the same thing with the a DOI, if the content of a string can be identified clearly as a DOI. At some point OWW may add support for the DOI in this manner. That would mean that Biblio references could contain them as well as any OWW string that either started with “doi:” or followed the word, “DOI” would lead to the article itself. Like Pubget, the resolution of a DOI to a particular publisher and their online repository for articles does require a subscription to the periodical. Another use of the DOI would be OWW issuing a DOI for a page. This bears more explanation. But also more research.

I’ll provide a simple example of a DOI lookup via a resolver if people are curious.




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