fishbase_archiver

Generates tabular archives for FishBase and SeaLifeBase tables using rOpenSci's FishBase API. Precompiled archives can be found in the releases section.

Please attribute Fishbase and SeaLifeBase when using the output of this archiver. You can find citation/ attribution guidelines on the respective webpages. At time of writing (Feb 2017), both Fishbase and SeaLifeBase was licensed under Creative Commons Attribution-Noncommercial 3.0 Unported License.

prerequisites

• linux, mac (tested on mac os x 10.11.5)
• bash / curl
• jq 1.5+ (see https://stedolan.github.io/jq/)

usage

Execute ./archive_fishbase.sh to compile the fishbase archives.

expected results

You'll see output like:

[https://fishbase.ropensci.org/stocks?offset=0&limit=5000] downloading...
[https://fishbase.ropensci.org/stocks?offset=0&limit=5000] downloaded.
returned: [5000], offset: [5000]
[https://fishbase.ropensci.org/stocks?offset=5000&limit=5000] downloading...
[https://fishbase.ropensci.org/stocks?offset=5000&limit=5000] downloaded.
returned: 5000, offset= 10000

After the script finishes, you'll find some archives in your work directory. Some examples look like:

species_sealifebase.tsv.gz
stocks_sealifebase.tsv.gz
taxa_sealifebase.tsv.gz
species_fishbase.tsv.gz
stocks_fishbase.tsv.gz
taxa_fishbase.tsv.gz

The archives are gzip compressed, tab separated files. The first few lines of stocks_fishbase.tsv.gz look like:

StockCode   SpecCode    StockDefs   StockDefsGeneral    Level   LocalUnique IUCN_Code   IUCN_Assessment Protected   StocksRefNo CITES_Code  CITES_Date  CITES_Ref   CITES_Remarks   Northernmost    NorthSouthN Southermost NorthSouthS Westernmost WestEastW   Easternmost WestEastE   BoundingRef BoundingMethod  TempMin TempMax TempRef EnvTemp Resilience  ResilienceRemark    pHMin   pHMax   pHRef   dHMin   dHMax   dHRef   GenBankID   RfeID   FIGIS_ID    EcotoxID    SCRFA_data  GMAD_ID SAUP    SAUP_ID SAUP_Group  AusMuseum   FishTrace   IUCN_ID IUCN_Group  BOLD_ID IGFAName    EssayID ICESStockID OsteoBaseID DORIS_ID    Aquamaps    Morphology  Occurrence  Strains Ecology Diseases    Abnorm  Metabolism  Predators   Spawning    Fecundity   Speed   Diet    Eggs    EggDevelop  Food    Larvae  LarvDyn LarvSpeed   PopDyn  LengthWeight    Gillarea    Maturity    MatSizes    Processing  Reproduction    Introductions   Abundance   Vision  Genetics    Aquaculture CountryComp Allele  GeneticStudies  Ration  Foods   Ecotoxicology   Brains  Catches FAOAqua LengthRelations LengthFrequency Sounds  Broodstock  EggNursery  FryNursery  LarvalNursery   Entered DateEntered Modified    DateModified    Expert  DateChecked TS
1884    6   Atlantic, Indian and Pacific:  in tropical and subtropical waters. Highly migratory species, Annex I of the 1982 Convention on the Law of the Sea (Ref. 26139). Atlantic, Indian and Pacific    species in general  Atlantic, Indian and Pacific:  in tropical and sub  LC  null    0   6376    null    null    null    null    47  N   38  S   180 W   180 E   54341   1   21  30  26  subtropical High    K=0.4-1.2; tm<1; tmax=5; Fec=85,000 null    null    null    null    null    null    34814   mh  3130    null    0   null    1   600006  1   384 0   154712  null    13788   Dolphinfish null    null    194 null    1   1   1   0   1   1   1   1   1   1   1   1   1   1   1   1   1   0   0   1   1   1   1   1   1   1   0   1   1   0   0   1   1   0   1   1   0   1   1   0   1   1   0   1   1   1   1   2   1990-10-18T00:00:00.000Z    949 2014-10-14T00:00:00.000Z    133 1996-02-27T00:00:00.000Z    null