FishBase/SeaLifeBase link to GoMexSi - species level

[FIN-JBarile]

@jsimons9 For this, the link to the corresponding species page in the GoMexSi site will be under the Internet Sources of the Species summary page. Please see image for example Scomberomorus cavalla.

Please advise location in GoMexSi web where FB/SLB will link to get interaction records/summary views. Thanks.

[jhpoelen]

As @FIN-JBarile mentioned by email, the related issues for links from GoMexSI to Fishbase/Sealifebase are documented here: https://github.com/GoMexSI/gomexsi-web/issues/72 and https://github.com/GoMexSI/gomexsi-web/issues/73 .

I imagine links into GoMexSI would use speccode (e.g. 120) instead of scientific name (e.g. Scomberomorus cavalla). The links to GloBI (and indirectly to GoMexSI) can be established by http://www.globalbioticinteractions.org/?interactionType=interactsWith&sourceTaxon=FBC%3AFB%3ASpecCode%3A120 where 120 is the spec code for species in question. I imagine that only species known to GloBI / GoMexSI should be used to avoid any links to empty results. This information is available through GloBI's taxonCache and interactions.tsv accessible through http://globalbioticinteractions.org/references . Both files are updated continuously, so the links would have to be updated once in a while.

Perhaps easiest to establish links to GloBI first (this linkage is already functional) - once GoMexSI implements required linking functionality (both incoming and outgoing), linking to GoMexSI should be as easy as changing the URL scheme and removing non-GoMexSI taxon links.

A GoMexSI link to lookup diet records would look same as what you'd link to from the summary page, something like: http://gomexsi.tamucc.edu/query-database/taxonomic/?subjectName=FBC%3AFB%3ASpecCode%3A120&allInteractions=on&findPrey=on&filterPrey=&findPredators=on&filterPredators=&serviceType=rest&action=rhm_data_query .

So, proposed steps:

1. establish method on fishbase/sealifebase to make a list of all fishbase speccodes that GloBI/GoMexSI have records for.
2. establish links to GloBI using (already implemented) lookup by speccode
3. once speccode lookups are supported by GoMexSI, include direct links from summary and diet pages to GoMexSI.

@FIN-JBarile @jsimons9 @dengaloo curious to hear your thoughts

[jsimons9]

Hi to all. Not sure where to start here. This issue has been dragging a bit. I am not sure that only having a link to GoMexSI under the FB/SLB Internet Resources will be sufficient. I don't know if this is possible, but what I was thinking is, for each GoMexSI reference for which we have diet data for a particular species, that a listing of the reference, and a summary of that data could be created in FB/SLB as you have already done for other references. At the end of the reference could be a link to GoMexSI that would provide the raw data from that reference. I would assume that the Fishbase species codes could be used as Jorrit suggests above. In some cases, the GoMexSI reference already exists in FB. In those cases, we would merely need to add the link to GoMexSI.

[FIN-JBarile]

@jsimons9 I created issue #105 for above comment. Please see if agreeable.

@jhpoelen In the coming update of FishBase and SeaLifeBase, the link to GloBi is implemented under Internet Sources in the Species Summary page. For FishBase we used the link as given above. For SeaLifeBase, we used this link: http://www.globalbioticinteractions.org/?interactionType=interactsWith&sourceTaxon=FBC%3ASLB%3ASpecCode%3A67017.

@dengaloo

[jhpoelen]

GloBI links look great. Please confirm that only SpecCode that appear in taxonCache (see http://globalbioticinteractions.org/references) are used. The reason for this is to avoid dead links into GloBI. Thanks for setting up the links from FB/SLB into GoMexSI and GloBI!

[FIN-JBarile]

@jhpoelen Confirming that links will only be active for speccodes that are in taxonCache.

[jhpoelen]

Great! Thanks!

[FIN-JBarile]

@jsimons9

The link to GoMexSi from the species summary page of FishBase, as described above, can be viewed at the Canada mirror of FishBase for now. For example the King mackerel

The link is labeled "GoMexSi (interaction data)", where the "GoMexSi" is hyperlinked to the GoMexSi homepage, and "interaction data" to the interaction query result.

Also, we provided another channel through the Tools section in the Search page. It is labeled "Species in GoMexSi". A page lists all species in FishBase that are in GoMexSi: http://www.fishbase.ca/gomexsilist.php?sort=species#.