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Template species interaction data repository compatible with globalbioticinteractions.org
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README.md

Build Status DOI GloBI

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. Create a repository from this template dataset using https://github.com/globalbioticinteractions/template-dataset/generate . Alternatively, you can fork this template dataset, but GitHub does not allow for forking a repository more than once for a specific account. If you do want multiple forks for your account, please see create multi-forks.
  2. Edit your README.md 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).
  5. Edit the name of your repository and description to make it easy for others to understand what your data is about.

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

Enable Automated Dataset Preservation/Publication

Preserving and publishing your valuable data is now easier than ever.

To enable automated preserving and publishing your data:

  1. login/register with zenodo
  2. enable automated preservation and publication of your dataset using instructions at https://zenodo.org/account/settings/github/ or https://guides.github.com/activities/citable-code/
  3. edit your zenodo publication and add it to zenodo's Global Biotic Interactions community.

For a completed example, see the publication of this template repository at DOI.

Enable Integration Testing

You can use http://travis-ci.org to check whether your data can be read by GloBI. This helps you to confirm that the changes you make in your GloBI data repository are compatible with GloBIs data processing pipeline.

To enable:

  1. make sure that the file .travis.yml is present in your repo. If not, copy the one available in https://github.com/globalbioticinteractions/template-dataset/blob/master/.travis.yml .
  2. go to http://travis-ci.org and login using your github credentials
  3. locate your data repository in your account list
  4. enable your data repository for travis
  5. now, trigger your first build by making a change in your repository
  6. confirm that travis-ci.org picks up on your changes

Now, whenever you make a change to data repository that is incompatible with GloBI, you receive a notification. If you'd like, you can include a build badge on your own html pages to see the health of your data. Here's an example of a build badge:

Build Status

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
argumentTypeId https://en.wiktionary.org/wiki/refute a URI that points to a definition of how this records support, refutes or provides other kind of arguments in the context of described interaction. When unspecified, the argument is assumed to be in support of the documented interaction claim.
argumentTypeName refute a human readable name that qualifies whether the record is in support or refutes of a particular interaction
sourceOccurrenceId 83742b5e-f0fd-4c12-a0af-c97191ea7722 globally unique id to reference the individual originating organism, specimen. Inspired by http://rs.tdwg.org/dwc/terms/#occurrenceID .
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
sourceBodyPartId http://purl.obolibrary.org/obo/UBERON_0000178 identifier of description of source body part is interacted with
sourceBodyPartName blood human readable description of source body part (e.g., "blood", "fruit")
sourceLifeStageId http://purl.obolibrary.org/obo/UBERON_0007023 identifier of description of source life stage
sourceLifeStageName adult human readable description of source life stage (e.g., "adult", "juvenile")
interactionTypeId RO:0002470 id of interaction as described by the OBO Relations Ontology
interactionTypeName eats human readable description of interactions
targetOccurrenceId a5ee64b5-081b-4fff-8adc-2b0c74b1f40a globally unique id to reference the individual target organism, specimen. Inspired by http://rs.tdwg.org/dwc/terms/#occurrenceID .
targetTaxonId EOL:1971 taxon classification id of target organism.
targetTaxonName Echinoidea scientific name of taxon classification of target organism of interaction
targetBodyPartId http://purl.obolibrary.org/obo/UBERON_0000178 identifier of description of target body part is interacted with
targetBodyPartName Echinoidea human readable description of target body part (e.g., "blood")
targetLifeStageId http://purl.obolibrary.org/obo/UBERON_0007023 identifier of description of target life stage
targetLifeStageName adult human readable description of target life stage (e.g., "adult", "juvenile")
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:10.1126/science.200.4340.403 Digital Object Id (DOI, http://doi.org) is commonly used to give papers, datasets or other digital object a permanent id
referenceUrl http://eol.org/data_objects/13596344 some resolvable url that point to information related to species interaction record
referenceCitation C. A. Simenstad, J. A. Estes, K. W. Kenyon, Aleuts, sea otters, and alternate stable-state communities, Science 200:403-411, from p. 404 (1978). 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:0002455 pollinates
RO:0002556 pathogen of
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