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:
- 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.
- Edit your
README.mdto describe your data in a human readable form.
- Ensure that your README.rd contains a reference to
- Edit your
globi.jsonto provide a machine readable description of your dataset (e.g. citation, license, version, files, format).
- 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:
- login/register with zenodo
- 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/
- edit your zenodo publication and add it to zenodo's Global Biotic Interactions community.
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.
- make sure that the file
.travis.ymlis present in your repo. If not, copy the one available in https://github.com/globalbioticinteractions/template-dataset/blob/master/.travis.yml .
- go to http://travis-ci.org and login using your github credentials
- locate your data repository in your account list
- enable your data repository for travis
- now, trigger your first build by making a change in your repository
- 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:
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.
|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.