Hyperlink related anatomy terms in anatomy term page about vfb

[dosumis]

Any system for hyperlinking has to be inconspicuous - text should be easily readable in raw marked up form as most consumers of ontology won't turn markup to hyperlinks.

There is a long standing proposal for marking up text in defs for hyperlinks: text goes in backticks
`` and are followed by ID in brackets. But perhaps it would make more sense to use Markdown. We could potentially use this to update names in defs, but it often makes sense to use shorter names in defs than the official ones.

[Robbie1977]

Without markup or some sort we could only feasibly resolve the abbreviations.

@dosumis would it be feasible to append instances of names and synonyms found in text fields with their FBbt ref in brackets during OWL creation? I could then make these links quite quickly.

[Robbie1977]

It would also be nice to still mark the name so it could be marked as non-translatable for google #237

[dosumis]

We have almost 2000 classes with an OBO-style FBbt ID in brackets in the definition, following the name in some form in the text. In almost all cases, the name is not delimited. It wouldn't be a huge job to write a perl script that searched for matches to names (& synonyms?) of the term in the preceding text and delimited those found. The most sensible way to do this would be to use Markdown link syntax. => name or maybe name. We could covert to a full URL, but this wouldn't be great for readability.

I wouldn't be keen to mine the text for matches to term names/synonyms and then automatically generate links - as I don't think this will be sufficiently reliable. We could mine as a way of generating lists of suggestions for hyperlinking that could then be reviewed by a curator.

[mmc46]

It would be good to hyperlink names and synonyms in text, but without adding FBbt ids or URLs to the text itself, please. That will make it hard to read the definition.

[Robbie1977]

Just putting square brackets around all terms would be satisfactory to resolve although I'd be happier if we precalculated and put the FBbt in the OWL version of the text when it's created to reduce the live processing.

[dosumis]

It would be good to hyperlink names and synonyms in text, but without adding FBbt ids or URLs to the text itself, please.

We already have almost 2000 classes with an OBO-style FBbt ID in brackets in the definition. Many of these are auto-rolled definitions, but some were manually added.

[dosumis]

BTW - auto-rolled don't appear in the editor's file.

[Robbie1977]

FBbt and also FBal all auto linked on the vfbdev site now.
Examples:
http://vfbdev.inf.ed.ac.uk/site/tools/anatomy_finder/index.htm?id=FBbt:00110858
http://vfbdev.inf.ed.ac.uk/site/tools/anatomy_finder/index.htm?id=FBbt:00110857

[Robbie1977]

Would be nicer to read if I could put the links on the names and then remove the refs in brackets.

If we could possibly square bracket the name before (at least on the auto-rolled ones) this would result in a more readable output?

[Robbie1977]

Also added FBti FBtp FBgn links - any more I should cover?

[mmc46]

I meant to add any more FBids to the ones already there.

I think it's just missing FBim

to link to

http://flybase.org/reports/FBimXXXXXXX.html

I could try changing the brackets. @dosumis would know if it might break something.

[dosumis]

Having the IDs in place and the names delimited in some way has two potential purposes. One is for hyperlinking, the other is that it gives us a way to keep names in text in sync. I'm not keen to remove the IDs in brackets as I'm not confident of automatically generating links based on lexical matching - given that names drift, and we often use shorter forms of names in text than when naming ontology classes.

If square brackets as delimiters are too distracting for consumers of the raw file, we could go with using backticks ( ` ) instead - as per the original proporal. I belive there are some OBO ontology dev groups who do this - most notably HPO.