{"id":22175053,"url":"https://github.com/andschar/taxalook","last_synced_at":"2026-05-16T00:37:25.684Z","repository":{"id":78397236,"uuid":"392745908","full_name":"andschar/taxalook","owner":"andschar","description":"An R Package and Database containing Information on Organisms","archived":false,"fork":false,"pushed_at":"2024-05-03T13:55:23.000Z","size":19,"stargazers_count":1,"open_issues_count":2,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-29T22:46:56.499Z","etag":null,"topics":["bioinformatics","biology","database","r"],"latest_commit_sha":null,"homepage":"","language":"R","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/andschar.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-08-04T15:49:51.000Z","updated_at":"2024-05-03T13:55:28.000Z","dependencies_parsed_at":null,"dependency_job_id":"f5db5a55-cf54-4794-a79e-a2a4cd3da0da","html_url":"https://github.com/andschar/taxalook","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andschar%2Ftaxalook","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andschar%2Ftaxalook/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andschar%2Ftaxalook/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andschar%2Ftaxalook/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/andschar","download_url":"https://codeload.github.com/andschar/taxalook/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245325220,"owners_count":20596818,"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":["bioinformatics","biology","database","r"],"created_at":"2024-12-02T07:55:55.756Z","updated_at":"2025-10-29T14:13:40.469Z","avatar_url":"https://github.com/andschar.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Taxa Lookup\n\nTaxa Lookup (`{taxalook}`) is a database and repository containing tabular information on\nspecies including their places of occurrence (e.g. countries, continents), their\nnatural habitats (e.g. freshwater) they are occurring in and other information.\n\n## Usage\n\nYou can use the R-package `{taxalook}` to query the database directly from\nR __OR__ you can download the data from its [Zenodo-Repository](https://zenodo.org/record/5948864).\n\n### From R\n\n#### Installation\n\n```r\nremotes::install_github('andschar/taxalook')\n```\n\n#### Example\n\nYou can query one or multiple taxa (or even all the taxa in the database by\nnot supplying a string) and you can add specific information on the taxa\ndepending on your requirements (e.g. `habitat = TRUE`).\n\n```r\nrequire(taxalook)\n\ntax = c('Pimephales promelas', 'Daphnia magna')\n\ntl_query(tax) # Only taxalook identifier and taxon name\ntl_query(tax, what = 'taxonomy') # Taxonomy information\ntl_query(tax, what = 'id') # Identifiers to other databases\ntl_query(tax, what = 'group') # Taxa convenient grouping\ntl_query(tax, what = 'habitat') # Habitat information\ntl_query(tax, what = 'continent') # Continent occurrence information\ntl_query(tax, what = 'country') # Country occurrence information\n```\n\n### Raw Data only\n\nAll the data tables are stored in the sub-directory __data__ as tab-separated\n(i.e. .tsv) and non-quoted files.\n\n| table            | description |\n|:-----------------|:------------|\n| tl_continent     | On which continent does a taxon occur ? |\n| tl_country       | In which country does a taxon occur ? |\n| tl_group         | To which group (e.g. algae, invertebrate) does a taxon belong to ? |\n| tl_habitat       | In which habitat does a taxon occur ? |\n| tl_id            | Table containing identifiers from other databases (e.g. GBIF, WORMS) |\n| tl_taxonomy      | Taxonomic classification |\n\nThe tables can be merged via the unique key column `tl_id`.\n\n## Contribute\n\nThe information here is by no means complete and users are highly encouraged to\ncontribute information to this database. Missing entries, wrong\nentries, more detailed information, you name it. Please signal issues via the [Issue](https://github.com/andschar/taxalook/issues) tracker.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandschar%2Ftaxalook","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fandschar%2Ftaxalook","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandschar%2Ftaxalook/lists"}