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osmose-model / osmose-web-api

Web service that generates Osmose configuration files from data sources like Fishbase and SeaLifeBase. Used by https://www.config.osmose-model.org .
MIT License
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introduce a way to map a group name to a specific species name / fishbase species id #9

Closed jhpoelen closed 8 years ago

jhpoelen commented 8 years ago

as suggested by @agruss2

Most users would want to decouple the groupname from the name of the examplar species.

agruss2 commented 8 years ago

@jhpoelen The "osm_param-species.csv" file indicates the names of focal functional groups using the "species.name.sp" keys. For instance, The "species.name.sp7" key is associated with the "CoastalOmnivores" value. I suggest that we introduce new keys in the "osm_param-species.csv" file, which we would call "species.reference.name.sp". For instance, "species.reference.name.sp7" would be "LagodonRhomboides". Please let me know if you like this idea. If so, I'll provide you with an updated version of the "osm_param-species.csv" file, so that you can test the bridge between FishBase/SeaLifeBase and OSMOSE with this new version of the file.

agruss2 commented 8 years ago

@jhpoelen @FIN-JBarile @Dengaloo In the "osm_param-species.csv" OSMOSE configuration file, I introduced new keys called "species.reference.name.sp". For instance, "species.reference.name.sp7" is "LagodonRhomboides". The new version of the "osm_param-species.csv" OSMOSE configuration file can be found in Dropbox in the "OSMOSE configuration files" folder. During our next phone call, we will need to discuss something important: If parameter estimates are unavailable for a reference species, we need to make sure that the bridge between FishBase/SeaLifeBase gets the missing parameter estimates from related species.

jhpoelen commented 8 years ago

@agruss2 Sound like good way to decouple the functional name from a focal species name. I would imagine that these pairs would be provided by the user. As far as the getting estimates from related species, I can imagine a couple of methods: resolve the focal species name, extract the genus, and see whether there's other species around in that genus. Alternatively, a more direct approach can be applied by making an exhaustive list of species that are known to overlap or share specific traits.

jhpoelen commented 8 years ago

@agruss2 suggest to turn the names into a list of names, so that fall-back names can be used if trait are not available for the primary name. (e.g. LagodonRhomboides,AriopsisFelis, instead of LagodonRhomboides).

FIN-JBarile commented 8 years ago

Please study the file that we propose for functional groups definitions, and tell us if that will work for this purpose.

Note: This is Deng and Skit responding together.

jhpoelen commented 8 years ago

I am assuming the functional group definition is part of another thread: please see https://github.com/jhpoelen/fb-osmose-bridge/issues/34#issuecomment-209213929 and my related comment.