refuteINAT: A repository from qgroom

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 your own data discoverable through GloBI:

Create a repository from this template dataset by visiting https://github.com/globalbioticinteractions/template-dataset/generate or clicking the "use this template" button.
Edit your README.md to describe your data in a human readable form.
Ensure that your README.md contains a reference to http://globalbioticinteractions.org.
Edit your globi.json to 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.

If you don't feel comfortable being indexed by GloBI because your data isn't ready yet, or no longer up-to-date, you can set "deprecated": true in globi.json to unlist (or opt-out) the dataset to be indexed and made visible via https://globalbioticinteractions.org (see globalbioticinteractions/globalbioticinteractions#372).

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.

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

Enable Integration Testing

You can use http://travis-ci.com 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:

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 .
go to http://travis-ci.com 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.com 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.

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")
sourcePhysiologicalStateId	http://purl.obolibrary.org/obo/PATO_0001422	identifier of description of source physiological state
sourcePhysiologicalStateName	dead	human readable description of source physiological state (e.g., "dead", "rotten")
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")
targetPhysiologicalStateId	http://purl.obolibrary.org/obo/PATO_0001422	identifier of description of target's phyiological state
targetPhysiologicalStateName	dead	human readable description of target's physiological state (e.g., "dead", "rotten")
habitatId	ENVO:00000067 or http://purl.obolibrary.org/obo/ENVO_00000067	reference to a habitat classification like Environmental Ontology (http://environmentontology.org/), Coastal and Marine Classification Standards (CMECS, https://iocm.noaa.gov/standards/cmecs-home.html).
habitatName	cave	human readable description of habitat
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
depth	123.2	distance below surface in meters
altitude	4553.2	height above sea level in meters
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.