Integrate IUCN Red List API: Add IUCN API endpoints, schema updates, and documentation for fetching species conservation status.

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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

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<T> {
   success: boolean;

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,
 });