Webinar: Database Planning, Structure & Sharing in Specify

[Grant]

Database Planning, Structure & Sharing in Specify

Presented by Grant Fitzsimmons, Technical Support Manager, Specify Collections Consortium, as part of the Specify Institutional Implementation Series.

Topics referenced in this webinar:

• Normalized vs. Denormalized Data
• What is a Collection Object
• Institutional Scoping/Data Sharing
  • Shared Resources
  • Object Relationships
  • Schema Config
  • Security & Permissions

Documentation

Scoping / Data Sharing Documentation

Specify Institutional Scopings

Institutional Scoping in Specify Specify supports data from multiple collections within a single database. For example, specimen records for fish and birds are combined within the same data tables of the database. For institutions with multiple collections, this storage model enables but does not grant access to data across multiple disciplines for most users. Users can have login and access privileges only for their collection data. Access to data across collections, disciplines, or divisions i…

Query Your Institutional Hierarchy

Query Your Institutional Hierarchy

See The Institutional Hierarchy Learn and read more about Institutional Scoping in Specify here. You can use the query below to find the structure present already in your database. [Institutional Hierarchy] Institutional Hierarchy Query.json (6.5 KB) Click on the Queries navigation menu item. Click New to create a new query. Click Import and select the ‘Institutional Hierarchy Query.json’ file downloaded from above. [Query Preview] [Query Results]

Slide Deck

Database Planning, Structure & Sharing in Specify.pdf (8.7 MB)

[jagullov]

In the webinar, I believe I understood that via API it is possible to perform joint searches across different collections that belong to different disciplines. Would it be possible to have an example of what such an API request should look like? For example, to know at certain levels of the storage tree hierarchy all the collection records that exist, since there are often spaces that share collections from different disciplines. Also, increasingly, lists of biodiversity are requested for different geographic levels (Locality, Municipality, and County).

Thanks in advance

[Grant]

Hi @jagullov,

Thanks for your question! We have our guide on how to use the Specify 7 API here:

How to use the Specify 7 API

This is a simple introduction to accessing the Specify API using the curl command line utility. For legibility, JSON output is piped through a pretty-printer provided by the Python json library. It is hoped that these examples illustrate how the API could be utilized by any environment which supports HTTP and JSON. These examples illustrate use with a demo server on localhost. Substitute an appropriate hostname as necessary. Swagger UI API Pages Within every instance of Specify 7, there i…

There is a section named Filtering which explains a bit more about this

@Grant

Filtering

Often it will be necessary to retrieve a collection of resources that meet certain criteria. The API implements basic filtering for this purpose. E.g. to retrieve all preparation records for CollectionObject with ID 12:

curl -b cookies.txt http://localhost:8000/api/specify/preparation/?collectionobject=12 \
    | python -m json.tool

Collection requests can also be filtered by domain, which means that only records which are in the same collection context as the user will be returned.

curl -b cookies.txt http://localhost:8000/api/specify/taxon/?domainfilter=true \
    | python -m json.tool

Effectively, if you do not add the ?domainfilter=true parameter to the API call, it will return records from all collections in the database. You can create scripts to find records from all collections that have preparations at a particular storage location (e.g. f"{BASE_URL}/api/specify/preparation/?storage={StorageID}"") or find all objects that have a locality at a particular level in the geography tree. It takes a bit of technical knowledge to accomplish, but it is completely doable!