From 093e8788da3e17b879e249d70ecb0a333fb7a35d Mon Sep 17 00:00:00 2001 From: Magnus-SmariSma <20734986-Magnus-SmariSma@users.noreply.replit.com> Date: Thu, 20 Mar 2025 22:19:01 +0000 Subject: [PATCH] Integrate IUCN Red List API: Add IUCN API endpoints, schema updates, and documentation for fetching species conservation status. Replit-Commit-Author: Agent Replit-Commit-Session-Id: e931b5ab-041b-42e7-baf1-50017869cef6 Replit-Commit-Screenshot-Url: https://storage.googleapis.com/screenshot-production-us-central1/e19c6a51-7e4c-4bb8-a6a6-46dc00f0ec99/339e2da6-2d1a-4412-8be5-d5f8e250ffde.jpg --- ...APIs-follow-these-steps--1742508730468.txt | 165 ++++++++++++++++++ client/src/lib/api.ts | 9 + shared/schema.ts | 6 + 3 files changed, 180 insertions(+) create mode 100644 attached_assets/Pasted-To-gather-detailed-information-about-species-by-connecting-to-multiple-APIs-follow-these-steps--1742508730468.txt diff --git a/attached_assets/Pasted-To-gather-detailed-information-about-species-by-connecting-to-multiple-APIs-follow-these-steps--1742508730468.txt b/attached_assets/Pasted-To-gather-detailed-information-about-species-by-connecting-to-multiple-APIs-follow-these-steps--1742508730468.txt new file mode 100644 index 0000000..7491bf2 --- /dev/null +++ b/attached_assets/Pasted-To-gather-detailed-information-about-species-by-connecting-to-multiple-APIs-follow-these-steps--1742508730468.txt @@ -0,0 +1,165 @@ +To gather detailed information about species by connecting to multiple APIs, follow these steps: + +## Step 1: Connect to GBIF API for Taxonomic and Occurrence Data + +1. **Install pygbif**: Use Python to install the `pygbif` library, which simplifies interactions with the GBIF API. + ```bash + pip install pygbif + ``` + +2. **Fetch Species Data**: Use the `species.name_lookup()` function to retrieve taxonomic information. + ```python + from pygbif import species + + # Example: Fetch data for 'Helianthus annuus' + data = species.name_lookup(q='Helianthus annuus', rank="species") + print(data) + ``` + +## Step 2: Connect to Wikidata Query Service for Biological Attributes + +1. **Access Wikidata Query Service**: Use the SPARQL endpoint at `https://query.wikidata.org/sparql`. + +2. **Query for Biological Attributes**: Use SPARQL to fetch attributes like lifespan or population. + ```sparql + # Example query to get lifespan of a species + PREFIX wdt: + PREFIX wd: + + SELECT ?item ?itemLabel ?lifespan + WHERE { + ?item wdt:P31 wd:Q15978631; # Species + wdt:P2114 ?lifespan. # Lifespan + SERVICE wikibase:label { bd:serviceParam wikibase:language "en". } + } + ``` + +## Step 3: Connect to IUCN Red List API for Conservation Status + +1. **Obtain an API Key**: Register at the IUCN Red List to get an API token. + +2. **Fetch Conservation Status**: Use the `iucnredlist` R package or the IUCN API directly. + ```r + # R example using iucnredlist package + library(iucnredlist) + + api <- init_api("your_api_key") + assessment_raw <- assessment_data(api, 266696959) + assessment <- parse_assessment_data(assessment_raw) + print(assessment) + ``` + +## Step 4: Connect to Swedish Biodiversity Data Infrastructure (SBDI) Bioatlas + +1. **Access SBDI Bioatlas**: Use the SBDI guides to access regional biodiversity data. + +2. **Fetch Regional Data**: Follow the step-by-step guides for using the Bioatlas APIs. + +## Step 5: Combine Data + +1. **Integrate Datasets**: Use programming languages like Python or R to merge data from different APIs based on species identifiers. + +2. **Analyze and Visualize**: Use libraries like Pandas, NumPy, and Matplotlib (Python) or dplyr and ggplot2 (R) to analyze and visualize the combined data. + +### Example Integration in Python + +```python +import pandas as pd +from pygbif import species + +# Fetch GBIF data +gbif_data = species.name_lookup(q='Helianthus annuus', rank="species") + +# Fetch Wikidata data using SPARQL (example query above) +# For simplicity, assume you have a function to execute SPARQL queries +wikidata_data = execute_sparql_query(query) + +# Fetch IUCN data (example using a hypothetical IUCN API function) +iucn_data = fetch_iucn_data(species_id) + +# Combine data into a single DataFrame +combined_data = pd.DataFrame({ + 'GBIF': gbif_data, + 'Wikidata': wikidata_data, + 'IUCN': iucn_data +}) + +# Print combined data +print(combined_data) +``` + +This approach allows you to gather comprehensive information about species by leveraging multiple APIs. + +Citations: +[1] https://pygbif.readthedocs.io/en/latest/modules/species.html +[2] https://techdocs.gbif.org/en/openapi/v1/species +[3] https://en.wikibooks.org/wiki/SPARQL/Wikidata_Query_Service +[4] https://www.wikidata.org/wiki/Wikidata:SPARQL_query_service/A_gentle_introduction_to_the_Wikidata_Query_Service +[5] https://iucn-uk.github.io/iucnredlist/ +[6] https://publicapi.dev/iucn-api +[7] https://docs.biodiversitydata.se/tutorials/step-by-step-help-guides/ +[8] https://biodiversitydata.se/explore-analyze/use-your-own-tools/our-apis/ +[9] https://data-blog.gbif.org/post/gbif-api-beginners-guide/ +[10] https://rdrr.io/github/bioatlas/SBDI4R/src/R/search_guids.R +[11] https://github.com/ManonGros/Small-scripts-using-GBIF-API +[12] https://www.youtube.com/watch?v=2h9LNS8C764 +[13] https://www.nies.go.jp/biowm/en/GBIFSpecies/ +[14] https://gbif.github.io/dwc-api/apidocs/org/gbif/dwc/terms/GbifTerm.html +[15] https://phylonext.github.io/inputdata/ +[16] https://github.com/gbif/gbif-api/issues/82 +[17] https://peerj.com/preprints/3304v1.pdf +[18] https://www.youtube.com/watch?v=netnQb-6F0M +[19] https://github.com/NaturalHistoryMuseum/gbif-name-resolution +[20] https://fairsharing.org/FAIRsharing.zv11j3 +[21] https://www.youtube.com/watch?v=TXdjxnjCvng +[22] https://stackoverflow.com/questions/39773812/how-to-query-for-people-using-wikidata-and-sparql +[23] https://query.wikidata.org +[24] https://www.youtube.com/watch?v=B59vEET-nEk +[25] https://www.wikidata.org/wiki/Wikidata:SPARQL_query_service/Wikidata_Query_Help +[26] https://librarycarpentry.github.io/lc-wikidata/05-intro_to_querying.html +[27] https://stackoverflow.com/questions/45316749/how-to-create-a-local-wikidata-query-service +[28] https://wikidataworkshop.github.io/2022/papers/Wikidata_Workshop_2022_paper_2349.pdf +[29] https://addshore.com/2019/10/your-own-wikidata-query-service-with-no-limits/ +[30] https://apiv3.iucnredlist.org +[31] https://api.iucnredlist.org/api-docs/index.html +[32] https://github.com/ropensci/rredlist +[33] https://cran.r-project.org/web/packages/rredlist/vignettes/rredlist.html +[34] https://pypi.org/project/IUCN-API/ +[35] https://apiv3.iucnredlist.org/api/v3/docs +[36] https://api.iucnredlist.org +[37] https://github.com/ropensci/rredlist/issues/52 +[38] https://github.com/biodiversitydata-se/repo-overview +[39] https://www.biodiversa.eu/wp-content/uploads/2024/01/Biodiversa-Governance-Sub-pilot-Sweden.pdf +[40] https://community.atlassian.com/t5/Atlassian-Home-questions/Can-we-interact-with-Atlas-API/qaq-p/2427472 +[41] https://biodiversitydata-se.github.io/r-tools-tutorial/ +[42] https://github.com/biodiversitydata-se/documentation-overview +[43] https://docs.beyondtrust.com/entitle/docs/configuring-mongodb-atlas-api-key +[44] https://docs.biodiversitydata.se/analyse-data/ +[45] https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2022.926623/full +[46] https://github.com/bioatlas/r-functionality/ +[47] https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6540eb2548dad23120c52242/original/the-hitchhiker-s-guide-to-statistical-analysis-of-feature-based-molecular-networks-from-non-targeted-metabolomics-data.pdf +[48] https://rdrr.io/github/bioatlas/SBDI4R/man/sbdi_lists.html +[49] https://royalsocietypublishing.org/doi/10.1098/rspb.2002.2218 +[50] https://docs.ropensci.org/rgbif/articles/gbif_sql_downloads.html +[51] https://github.com/ManonGros/Small-scripts-using-GBIF-API/blob/master/query_species_list/functions_query_from_species_list.py +[52] https://techdocs.gbif.org/en/openapi/ +[53] https://aubreymoore.github.io/blog/posts/using-the-species-api-to-mine-the-gbif-backbone-taxonomy/ +[54] https://tutorials.inbo.be/tutorials/r_gbif_checklist/ +[55] https://metacpan.org/dist/App-wdq/view/script/wdq +[56] https://www.mediawiki.org/wiki/Wikidata_Query_Service/User_Manual/ru +[57] https://www.mediawiki.org/wiki/Wikidata_Query_Service/User_Manual +[58] https://wikitech.wikimedia.org/wiki/Wikidata_Query_Service +[59] https://flograttarola.com/post/rbiodiversidata/ +[60] https://publicapis.io/iucn-species-database-api +[61] https://cran.r-project.org/web/packages/rredlist/rredlist.pdf +[62] https://github.com/CerrenRichards/IUCN-Threats +[63] https://git-og.github.io/EasyOpenRedList/ +[64] https://www.youtube.com/watch?v=4T6GXtptmj4 +[65] https://academic.oup.com/nargab/article/5/1/lqad003/6997971 +[66] https://docs.biodiversitydata.se/tutorials/step-by-step-help-guides/setting-up-and-using-your-sbdi-bioatlas-account/ +[67] https://apidocs.tbauctions.com/getting-started +[68] https://biodiversitydata-se.github.io/mol-data/ +[69] https://www.biorxiv.org/content/10.1101/2022.08.29.505468.full + +--- +Answer from Perplexity: pplx.ai/share \ No newline at end of file diff --git a/client/src/lib/api.ts b/client/src/lib/api.ts index 65cc97b..27ba000 100644 --- a/client/src/lib/api.ts +++ b/client/src/lib/api.ts @@ -8,6 +8,15 @@ export const CITES_API_ENDPOINTS = { REFERENCES: "references" }; +export const IUCN_API_ENDPOINTS = { + BASE_URL: "https://apiv3.iucnredlist.org/api/v3", + SPECIES: "species", + SPECIES_BY_NAME: "species/name", + THREATS: "threats/species/name", + CONSERVATION_MEASURES: "measures/species/name", + HABITATS: "habitats/species/name" +}; + // API types export interface ApiResponse { success: boolean; diff --git a/shared/schema.ts b/shared/schema.ts index bea86eb..5de257f 100644 --- a/shared/schema.ts +++ b/shared/schema.ts @@ -15,6 +15,9 @@ export const species = pgTable("species", { genus: text("genus"), citesListings: jsonb("cites_listings"), citesId: integer("cites_id"), + iucnStatus: text("iucn_status"), + iucnId: text("iucn_id"), + iucnData: jsonb("iucn_data"), apiData: jsonb("api_data"), searchedAt: timestamp("searched_at").defaultNow(), }); @@ -31,6 +34,9 @@ export const insertSpeciesSchema = createInsertSchema(species).pick({ genus: true, citesListings: true, citesId: true, + iucnStatus: true, + iucnId: true, + iucnData: true, apiData: true, });