README.md

In kevinlove/idb-us-collections: Interface to the iDigBio Collections API

iDigBio: US Collections

iDigBio publishes a list of US Collections, via the iDigBio Portal, that is intended to be a comprehensive list of all natural history collections in the United States of America. This GitHub project provides an administrative interface for managing the publishing of this list and offers tools to those who would like to use these data programmatically.

API Endpoint

Published collections JSON Endpoint

Project Structure

Collections should each have their own JSON file, named by their collection UUID, and be formatted similar to this:

[
  {
    "institution": "Yale University, Peabody Museum of Natural History",
    "collection": "Historical Scientific Instruments",
    "recordsets": "",
    "institution_code": "",
    "collection_code": "",
    "collection_uuid": "urn:uuid:09b5acf0-899b-4b4d-abd0-7dbb7799053c",
    "collection_lsid": "NA",
    "collection_url": "http://peabody.yale.edu/collections/historical-scientific-instruments",
    "collection_catalog_url": "http://peabody.yale.edu/collections/search-collections?hsi",
    "contact": "Paola Bertucci",
    "contact_role": "Assistant Curator",
    "contact_email": "[e-mail]",
    "taxonomic_coverage": "",
    "geographic_range": "",
    "collection_size": "",
    "mailing_address": "Yale University, PO Box 208118",
    "mailing_city": "New Haven",
    "mailing_state": "Connecticut",
    "mailing_zip": "06511-0000",
    "physical_address": "170-210 Whitney Avenue",
    "physical_city": "New Haven",
    "physical_state": "Connecticut",
    "physical_zip": "06511-0000",
    "update_url": "https://docs.google.com/forms/d/1slWOvxuLpuPdvDihSibLQq9BPsOqPzK8Hh93zCW3dRI/viewform?entry.823080433=the+collection+is+already+in+the+list&entry.764919322=urn:uuid:09b5acf0-899b-4b4d-abd0-7dbb7799053c&entry.326174790=Yale University, Peabody Museum of Natural History&entry.2031121141=Historical Scientific Instruments&entry.4068754=&entry.1582913154=&entry.1336841557=http://peabody.yale.edu/collections/historical-scientific-instruments&entry.103879345=http://peabody.yale.edu/collections/search-collections?hsi&entry.107456176=&entry.879476273=&entry.417603227=&entry.1321049572=Paola Bertucci&entry.1687847097=Assistant Curator&entry.1086198428=[e-mail]&entry.246950189=Yale University, PO Box 208118&entry.1584255348=New Haven&entry.1966582743=Connecticut&entry.256217142=06511-0000&entry.447546773=170-210 Whitney Avenue&entry.1565624766=New Haven&entry.1920508789=Connecticut&entry.1022645685=06511-0000",
    "lat": 41.3167,
    "lon": -72.9204
  }
]

Metadata

• In general, institution and collection names should be spelled in full including the first/middle names of the people which the collections are named after. This is intended to facilitate full name search and avoid ambiguities, e.g.: -- Bernice Pauahi Bishop Museum and not B.P. Bishop Museum or Bishop Museum
• institution: name of the institution, ordered in decreasing hierarchy, separated by commas, e.g.: -- University of Florida, Florida Museum of Natural History -- Brigham Young University, Monte L. Bean Life Science Museum
• collection: name of the collection, ordered in decreasing hierarchy, separated by commas MAIN denotes the record for the institution itself rather than one of the collections If the institution itself is just an herbarium, it should be listed as Herbarium (not MAIN)
• recordsets the record sets for the collection in iDigBio. They should be separated by commas
• institution_code the institution code. We are using the GRbio convention of adding as a suffix if it’s a collection listed in index herbariorum
• collection_code the prefix used by the collection in their catalog number
• collection_uuid generated by us, should be unique, with prefix urn:uuid:
• institution_lsid the GRbio LSID or coolURI for the collection, empty fields are collections that were not part of GRbio as of August 2014
• collection_url the URL of the website that lists general information about the collection
• ccollection_catalog_url the URL of the website that provides a search interface (or lists specimens) for the specimens housed by the collection
• contact preferred person to act as point of contact for the collection. Usually I have removed titles from this field to only keep the name
• contact_role role of the contact person for the collection
• contact_email email of the contact person
• taxonomic_coverage taxonomic strengths of the collection
• geographic_range the geographic range from which the specimens in the collection come from.
• collection_size the number of specimens/lots in the collection
• mailing_address mailing address for the collection
• mailing_city
• mailing_state
• mailing_zip to avoid conversion issue between spreadsheet formats, zip codes starting with a 0 have -0000 at the end: e.g., 02138-0000 for the MCZ
• physical_address: physical address for the collection
• physical_city
• physical_state
• physical_zip to avoid conversion issue between spreadsheet formats, zip codes starting with a 0 have -0000 at the end: e.g., 02138-0000 for the MCZ
• lat decimal latitude for the collection, should only be added for collection addresses that fail the geolocation lookup with the API
• lon decimal longitude for the collection, should only be added for collection addresses that fail the geolocation lookup with the API

Stub records

Stub records can be generated using the function r createCollStub . A stub record will be generated and added to a directory called "stubs". These stub records will have UUID's and can be moved to the "collections" directory once they have been updated or are complete.

{
  "institution": "",
  "collection": "",
  "recordsets": "",
  "institution_code": "",
  "collection_code": "",
  "collection_uuid": "",
  "collection_lsid": "",
  "collection_url": "",
  "collection_catalog_url": "",
  "contact": "",
  "contact_role": "",
  "contact_email": "",
  "taxonomic_coverage": "",
  "geographic_range": "",
  "collection_size": "",
  "mailing_address": "",
  "mailing_city": "",
  "mailing_state": "",
  "mailing_zip": "",
  "physical_address": "",
  "physical_city": "",
  "physical_state": "",
  "physical_zip": "",
  "update_url": "",
  "lat": 0,
  "lon": 0
}

kevinlove/idb-us-collections documentation built on May 20, 2019, 9:07 a.m.