Skip to content

Latest commit

 

History

History
52 lines (39 loc) · 4.41 KB

README.md

File metadata and controls

52 lines (39 loc) · 4.41 KB
Raw

DOI

This repository provides an example on how to make your interaction data available through Global Biotic Interactions (GloBI, http://globalbioticinteractions.org).

If you have comments or questions please open an issue.

Share Your Interaction Data

If you want to share your own data through GloBI:

  1. Fork this repository.
  2. Edit your README.rd to describe your data in a human readable form.
  3. Ensure that your README.rd contains a reference to http://globalbioticinteractions.org.
  4. Edit your globi.json to provide a machine readable description of your dataset (e.g. citation, license, version, files, format).

After you do this, the data will be available through GloBI within a day or so.

Data Format and Dictionary

The file interactions.tsv is a suggestion on how to encode your interaction data using a tab separated file format (tsv) in combination with columns described below. This provides an example on how to capture your data in a human and machine friendly way and keep it relatively doable to update the file using a basic text editor. Other formats are supported, just let us know about the syntax, and we'll make it work.

Each term has two columns: one for an id and another for a label. The former is to make the term machine readable, the latter to make is easy to read for humans. With both id and name present possible typos or other transcription errors can be detected with a (somewhat) straightforward algorithm.

term example description
sourceTaxonId EOL:328583 taxon classification id of originating organism in some taxon name authority
sourceTaxonName Enhydra lutris scientific name of taxon classification of originating organism
interactionTypeId RO:0002470 id of interaction as described by the OBO Relations Ontology
interactionTypeName eats human readable description of interactions
targetTaxonId EOL:1971 taxon classification id of originating organisms
targetTaxonName Echinoidea scientific name of taxon classification of target organism of interaction
LocationinhostName On tube feet The location of the host where the parasite is found
localityId GEONAMES:5391961 reference to geo classification like geonames.org, gazetteer or other.
localityName San Francisco Bay, California, USA human readable description of locale
decimalLatitude -41.0983423 latitude of geographic center of interaction observation location http://rs.tdwg.org/dwc/terms/index.htm#decimalLatitude
decimalLongitude -121.1761111 longtide of geographic center of interaction observation location http://rs.tdwg.org/dwc/terms/index.htm#decimalLongitude
observationDateTime 2014-11-18T06:37:04Z ISO 8601 formatted date time string
referenceDoi doi:10.3354/dao002147 Digital Object Id (DOI, http://doi.org) is commonly used to give papers, datasets or other digital object a permanent id
referenceCitation Jangoux, M. 1986 Diseases of Echinodermata. I. Agents microorganisms and protistans Diseases of Aquatic Organisms (Impact Factor: 1.59) 2:147-162. doi:10.3354/dao002147 human readable reference

Term Id Sources

Rather than only supplying a name for a taxon and/or locality, a reference to some established taxonomy and/or geo database is preferred. Commonly used taxon id sources include, but are not limited to GBIF, EOL, ITIS and WoRMS. Geo database or vocabularies include geonames and Gazetteer Ontology.

Interaction Id Cheatsheet

For more terms, please see OBO Relations Ontology.

interactionTypeId interactionTypeName
RO:0002470 eats
RO:0002444 parasite of
RO:0002456 pollinates
RO:0002556 pathogen of