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| # This workflow will review a GloBI indexed dataset. | ||
| # For more information see: https://globalbioticinteractions.org | ||
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| name: GloBI review by Elton | ||
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| on: | ||
| push: | ||
| branches: [ '*' ] | ||
| pull_request: | ||
| branches: [ '*' ] | ||
| schedule: | ||
| - cron: "0 0 * * 1" | ||
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| jobs: | ||
| review: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up JDK 1.8 | ||
| uses: actions/setup-java@v3 | ||
| with: | ||
| distribution: 'temurin' | ||
| java-version: '8' | ||
| - name: download review script | ||
| run: curl --silent -L "https://raw.githubusercontent.com/globalbioticinteractions/globinizer/master/check-dataset.sh" > check-dataset.sh | ||
| - name: download network compiler script | ||
| run: | | ||
| curl --silent -L "https://raw.githubusercontent.com/globalbioticinteractions/globinizer/master/compile-network.sh" > compile-network.sh | ||
| chmod +x compile-network.sh | ||
| - name: review dataset | ||
| run: bash check-dataset.sh "${GITHUB_REPOSITORY}" | ||
| - name: Share review report | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: review-report | ||
| path: | | ||
| README.txt | ||
| datasets/ | ||
| index.* | ||
| indexed-* | ||
| review* |
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| .elton/ | ||
| add_travis_artifact_upload_keys.sh | ||
| datasets/ |
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| # | ||
| # To enable uploading reviews into a S3 compatible | ||
| # bucket, please use the travis-ci.org commandline | ||
| # tool, substitute the replace_me values and | ||
| # run the following to add the required | ||
| # environment variables to your travis configuration. | ||
| # | ||
| # Also see https://github.com/globalbioticinteractions/globinizer | ||
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| travis encrypt ARTIFACTS_KEY=replace_me_with_aws_key | ||
| travis encrypt ARTIFACTS_SECRET=replace_me_with_aws_secret | ||
| travis encrypt ARTIFACTS_BUCKET=replace_me_with_aws_bucket | ||
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| install: | ||
| - curl -L "https://raw.githubusercontent.com/globalbioticinteractions/globinizer/master/check-dataset.sh" | ||
| > check-dataset.sh | ||
| - chmod +x check-dataset.sh | ||
| script: "./check-dataset.sh ${TRAVIS_REPO_SLUG}" |
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| [](../../actions/workflows/review.yml) [](https://zenodo.org/badge/latestdoi/26293374) [](https://globalbioticinteractions.org/?accordingTo=globi:globalbioticinteractions/template-dataset) | ||
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| This repository provides an example on how to make your interaction data available through Global Biotic Interactions (GloBI, http://globalbioticinteractions.org). | ||
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| If you have comments or questions please [open an issue](https://github.com/globalbioticinteractions/globalbioticinteractions/issues/new). | ||
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| ## Share Your Interaction Data | ||
| If you want to make your own data discoverable through GloBI: | ||
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| 1. Create a repository from this template dataset by visiting https://github.com/globalbioticinteractions/template-dataset/generate or clicking the "use this template" button. | ||
| 2. Edit your ```README.md``` and describe your data in a human readable form. | ||
| 3. Ensure that your README.md 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. | ||
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| After you do this, the data will be available through GloBI within a day or so. | ||
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| 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 https://github.com/globalbioticinteractions/globalbioticinteractions/issues/372). | ||
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| ## Enable Automated Dataset Preservation/Publication | ||
| Preserving and publishing your valuable data is now easier than ever. | ||
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| To enable automated preserving and publishing your data: | ||
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| 1. login/register with [zenodo](https://zenodo.org) | ||
| 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](https://zenodo.org/communities/globalbioticinteractions/). | ||
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| For a completed example, see the publication of this template repository at [](https://zenodo.org/badge/latestdoi/26293374). | ||
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| ## Enable Integration Testing | ||
| Integration testing, also known as "GloBI review by Elton", is currently supported through GitHub actions, and is enable automatically. | ||
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| If you'd like to learn more about GitHub actions in general, please see https://github.com/features/actions . For reviewing the review script, please see [./.github/workflows/review.yml](./.github/workflows/review.yml). You'll find that most of the review logic is captured in [https://github.com/globalbioticinteractions/globinizer/blob/master/check-dataset.sh](https://github.com/globalbioticinteractions/globinizer/blob/master/check-dataset.sh) . | ||
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| For any remaining questions about the review process, please [open an issue](https://github.com/globalbioticinteractions/globalbioticinteractions/issues) or contact folks [by email](https://globalbioticinteractions.org/contribute). There's plenty of ways to review species interaction datasets, and your questions, ideas and suggestions help to find more intuitive ways to do so. Thank in advance for sharing your ideas! | ||
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| By the way, on a successful review, you should see a badget similar to the one below: | ||
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| 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 "green" review badge: | ||
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|  | ||
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| However, if you see a "red" review badge like: | ||
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|  | ||
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| please check your review logs, or ask questions if you'd like to have some guidance on how to access or interpret the review reports. | ||
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| ## Data Format and Dictionary | ||
| The file [interactions.tsv](./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. | ||
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| 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. | ||
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| 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 | ||
| sourceTaxonKingdomName | Animalia | name of kingdom of taxon classification of originating organism | ||
| sourceTaxonPhylumName | Chordata | name of phylum of taxon classification of originating organism | ||
| sourceTaxonClassName | Gastropoda | name of class of taxon classification of originating organism | ||
| sourceTaxonOrderName | Carnivora | name of order of taxon classification of originating organism | ||
| sourceTaxonFamilyName | Mustelidae | name of family of taxon classification of originating organism | ||
| sourceTaxonGenusName | Enhydra | name of genus of taxon classification of originating organism | ||
| sourceTaxonSpecificEpithetName | lutris | name of specific epithet of taxon classification of originating organism | ||
| sourceTaxonSubspecificEpithetName | nereis | name of subspecific epithet 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](https://github.com/oborel/obo-relations) | ||
| 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 | ||
| targetTaxonKingdomName | Animalia | name of kingdom of taxon classification of target organism of interaction | ||
| targetTaxonPhylumName | Chordata | name of phylum of taxon classification of target organism of interaction | ||
| targetTaxonClassName | Gastropoda | name of class of taxon classification of target organism of interaction | ||
| targetTaxonOrderName | Carnivora | name of order of taxon classification of target organism of interaction | ||
| targetTaxonFamilyName | Mustelidae | name of family of taxon classification of target organism of interaction | ||
| targetTaxonGenusName | Enhydra | name of genus of taxon classification of target organism of interaction | ||
| targetTaxonSpecificEpithetName | lutris | name of specific epithet of taxon classification of target organism of interaction | ||
| targetTaxonSubSpecificEpithetName | nereis | name of subspecific epithet 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](https://en.wikipedia.org/wiki/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 | ||
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| ## 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](http://gbif.org), [EOL](http://eol.org), [ITIS](http://itis.gov) and [WoRMS](http://marinespecies.org). Geo database or vocabularies include [geonames](http://geonames.org) and [Gazetteer Ontology](http://bioportal.bioontology.org/ontologies/GAZ). | ||
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| ## Interaction Id Cheatsheet | ||
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| For more terms, please see [OBO Relations Ontology](https://github.com/oborel/obo-relations). | ||
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| interactionTypeId | interactionTypeName | ||
| --- | --- | ||
| [RO:0002470](http://www.ontobee.org/browser/rdf.php?o=RO&iri=http://purl.obolibrary.org/obo/RO_0002470) | eats | ||
| [RO:0002444](http://www.ontobee.org/browser/rdf.php?o=RO&iri=http://purl.obolibrary.org/obo/RO_0002444) | parasite of | ||
| [RO:0002455](http://www.ontobee.org/browser/rdf.php?o=RO&iri=http://purl.obolibrary.org/obo/RO_0002455) | pollinates | ||
| [RO:0002556](http://www.ontobee.org/browser/rdf.php?o=RO&iri=http://purl.obolibrary.org/obo/RO_0002556) | pathogen of |
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| { | ||
| "_comment": "Sample GloBI dataset descriptor. See http://github.com/globalbioticinteractions for more information.", | ||
| "citation": "Jorrit H. Poelen. 2014. Species associations manually extracted from literature.", | ||
| "deprecated": false | ||
| } |
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