jhpoelen
commented
8 years ago Hi @agruss2 . I took a first stab at implementing a first bridge with FishBase.
Just now, I generated a dynamic configuration using: https://fbob.herokuapp.com/osmose_config.zip?htlGroupName=ScomberomorusCavalla&htlGroupName=LutjanusCampechanus&htlGroupName=EpinephelusMorio
I found that the following osmose parameters were populated in the osm_param-species.csv file:
| param name | value |
|---|---|
| ... | ... |
| species.lifespan.sp0 | 14 |
| species.lifespan.sp1 | 57 |
| species.lifespan.sp2 | 25 |
| ... | ... |
where sp0 is Scomberomorus cavalla , sp1 is Lutjanus campechanus and sp2 is Epinephelus morio .
Note that the values are extracted by name, meaning that a species name must be provided using the group name: [Genus][Specific epithet] with the epithet being capitalized. For instance, when using Scomberomorus cavalla as a examplar species for a group, the groupName must be ScomberomorusCavalla for the fishbase bridge to be activated.
The mapping to the osmose parameters are captured in the following file: https://github.com/jhpoelen/fb-osmose-bridge/blob/master/src/main/resources/com/github/jhpoelen/fbob/fishbase-mapping.csv
As discussed with @agruss2 , the first parameter we'd like to pre-populate from Fishbase/SeaLifeBase is lifespan (or max age).
We'd lookup the lifespan using the name provided for the higher trophic level group name. For instance, when a name Scomberomorus cavalla is provided, it'll extract information from (first?) Tmax parameter as retrieved from http://www.fishbase.se/PopDyn/PopCharList.php?ID=120&GenusName=Scomberomorus&SpeciesName=cavalla&fc=416 .