{"id":29088759,"url":"https://github.com/belgianbiodiversityplatform/natagora-occurrences","last_synced_at":"2025-07-06T00:35:25.148Z","repository":{"id":68521925,"uuid":"177742437","full_name":"BelgianBiodiversityPlatform/natagora-occurrences","owner":"BelgianBiodiversityPlatform","description":"🦆 Observations.be - Species occurrence datasets published by Natagora","archived":false,"fork":false,"pushed_at":"2021-09-17T14:39:04.000Z","size":44,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-06-28T03:38:34.734Z","etag":null,"topics":["dataset","gbif","occurrences","sql"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BelgianBiodiversityPlatform.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-03-26T08:11:33.000Z","updated_at":"2021-09-17T14:39:07.000Z","dependencies_parsed_at":null,"dependency_job_id":"f9ad45e7-e7b8-4783-8ed9-74d90127415e","html_url":"https://github.com/BelgianBiodiversityPlatform/natagora-occurrences","commit_stats":{"total_commits":28,"total_committers":3,"mean_commits":9.333333333333334,"dds":0.2857142857142857,"last_synced_commit":"9d6b980914bf1ce96375d57ac1f06c538e682730"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/BelgianBiodiversityPlatform/natagora-occurrences","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BelgianBiodiversityPlatform%2Fnatagora-occurrences","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BelgianBiodiversityPlatform%2Fnatagora-occurrences/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BelgianBiodiversityPlatform%2Fnatagora-occurrences/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BelgianBiodiversityPlatform%2Fnatagora-occurrences/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BelgianBiodiversityPlatform","download_url":"https://codeload.github.com/BelgianBiodiversityPlatform/natagora-occurrences/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BelgianBiodiversityPlatform%2Fnatagora-occurrences/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263832178,"owners_count":23517347,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["dataset","gbif","occurrences","sql"],"created_at":"2025-06-28T03:32:40.588Z","updated_at":"2025-07-06T00:35:25.102Z","avatar_url":"https://github.com/BelgianBiodiversityPlatform.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Observations.be - Species occurrence datasets published by Natagora\n\n## Rationale\n\nThis repository contains the functionality to standardize datasets of [observations.be](https://observations.be) to [Darwin Core Occurrence](https://www.gbif.org/dataset-classes) datasets that can be harvested by [GBIF](http://www.gbif.org). It was originally developed for the [TrIAS project](http://trias-project.be).\n\n## Workflow\n\n[observations.be](https://observations.be) database → Darwin Core SQL view → Direct connection with the IPT or CSV upload\n\n## Datasets\n\nTitle (and GitHub directory) | IPT | GBIF\n--- | --- | ---\n[Observations.be - Non-native species occurrences in Wallonia, Belgium](datasets/natagora-alien-occurrences) | [natagora-alien-occurrences](https://ipt.biodiversity.be/resource?r=natagora-alien-occurrences) | \u003chttps://doi.org/10.15468/p58ip1\u003e\n[Observations.be - Orthoptera occurrences in Wallonia, Belgium](datasets/natagora-orthoptera-occurrences) | [natagora-orthoptera-occurrences](https://ipt.biodiversity.be/resource.do?r=natagora-orthoptera-occurrences) | \u003chttps://doi.org/10.15468/r763pb\u003e\n\n## Repo structure\n\nThe structure for each dataset in [datasets](datasets) is based on [Cookiecutter Data Science](http://drivendata.github.io/cookiecutter-data-science/) and the [Checklist recipe](https://github.com/trias-project/checklist-recipe). Files and directories indicated with `GENERATED` should not be edited manually.\n\n```\n├── sql                      : Darwin Core SQL queries\n│\n└── specs                    : Whip specifications for validation\n```\n\n[references](references) contains controlled vocabularies for:\n\n- [behavior](references/behavior.csv)\n- [lifeStage](references/lifeStage.csv)\n- [occurrenceRemarks](references/occurrenceRemarks.csv)\n- [reproductiveCondition](references/reproductiveCondition.csv)\n- [samplingProtocol](references/samplingProtocol.csv)\n\nThese are shared with the [waarnemingen.be datasets](https://www.gbif.org/dataset/search?q=waarnemingen.be).\n\n## Validating with whip\n\nPublished data can be validated with [whip](https://github.com/inbo/whip):\n\n1. Download the published DwC Archive from the IPT\n2. Unzip the data in the directory `data` (git ignored), so data are available at `data/data_file.txt`\n3. In terminal, start `jupyter notebook` from the repository root\n4. Open `notebooks/whip.ipynb`\n5. In the notebook, set the correct paths at the top of the file\n6. Run the notebook\n7. Update dataset or specifications until they align\n\n## Contributors\n\n[List of contributors](https://github.com/trias-project/natagora-occurrences/contributors)\n\n## License\n\n[MIT License](https://github.com/trias-project/natagora-occurrences/blob/master/LICENSE)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbelgianbiodiversityplatform%2Fnatagora-occurrences","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbelgianbiodiversityplatform%2Fnatagora-occurrences","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbelgianbiodiversityplatform%2Fnatagora-occurrences/lists"}