specifysystems / syftorium

Repository for the Specify Systems Syftorium API endpoint

syftorium

Repository for the Specify Systems Syftorium API endpoint

Welcome to the Syftorium!

The Syftorium is a collection of specimen-based analytics assessing the composition of collection holdings and available species information. These data are used to compare and assess collections against and among the collective holdings of all of the world's data that we can get our hands on. This information is then made available back to the institutions and others so that it can assist those collections in prioritizing collecting and digitization efforts, institutional loans, mergers, deaccessions, et cetera in order to improve, or show off, the overall quality of the collection. This information can also be used by the community as a whole to identify gaps in species knowlege and redundancies for similar motivations. The Syftorium presents this information in multivariate-, but subsettable, space in order to create the most compelling picture of the data as possible in order to provide as much value and feedback to the community as we can.

Using the Syftorium

Syftorium web services are documented using the Open API 3 spec. The raw documentation can be found at /docs/openapi.yml and a version rendered with Swagger can be found at https://lifemapper.github.io/lmsyft/.

syftorium's Issues

Add mapserver to syftorium machine

We will use mapserver to serve maps for at least this version of the syftorium. Please add it to the installation.

Implement a GET endpoint for Syftorium outputs

This output will evolve over time but should be accessible via a GET request to retrieve the statistics, images, etc that we have.

Implement Syftorium computation storage mechanism

This will almost definitely be a direct access to the storage for the computations and not through the main API but we need a mechanism to store our outputs from Syftorium computations.

Design and implement Solr index for version 1 of GET services

This index will include collection, specimen, and probably species indecies. It should be in Solr for this first versoin

Define the API for version 1 of Syftorium GET services

We established what is likely to be the services that we expose with version 1 of Syftorium GET services in a Google doc. Document what the API should look like using openapi.

Include examples in the documentation so that Specify and others can start working against it before the services are live.

Evaluate computations, index, and APIs of version 1 of GET services

Determine what works and what doesn't so we can improve for the next version.

Create initial Syftorium computations Docker container

We have decided to, at a minimum, experiment with Docker containers as a means for distributing Syftorium computations (and more?)

Set it up to build on tags probably

Implement computations for version 1 of GET services

Implement computations for this version to enable the services defined for version 1

• specimen-based computations
• species-based computations
• collection-based computations

Create tool for posting analysis outputs to the Solr index

We will need to post the outputs of syftr computations to the index. To do so, we will need some sort of tool that POSTs the data to Solr. This may be built in to the solr distribution.