Search Interface

https://hyde.cyverse.org/isamples_central/ui

Prototyping

https://find.isample.xyz/

Overview

Containerized

System

Current Deployment

Hierarchical

Multiple "Centrals"

Supporting Content Creation

• Sample record creation
• Minting identifiers
  • pre-allocation
  • retention with samples
  • accumulation of information
  • sub-samples, processing, analysis, publication
• Seamless ingest to collections
• Flow through to iSB, iSC

Common Sampling Workflow

Workflow with preallocated identifiers

iSamples Sampling Support

Core model

• Model definitions in LinkML
  • Vocabularies defined in SKOS
  • GeoJSON, other standard structures
• Models used for:
  • Mapping source to iSamples Core
  • Index construction
  • Defining user interfaces
  • Sample staging
• Extended for experiment / community demands

Notes

Sampling support

The staging area is constructed with input from the community defined models, and uses identifiers pre-allocated from an ID authority using authorization provided by the creator or the collection. After populating the sample staging (and content validation), the content is loaded ("published") to the collection. This operation also moves the pre-allocated identifiers from a provisional to "published" or "non-provisional" status. iSB subsequently retrieves the content and makes it available to iSC through the normal synchronization workflow.

The sample staging area is an environment that facilitates data collection by the researcher. It is informed by the community data models, and also by common APIs and functionality needed to support reliable capture of the content, mint identifiers, validate content, and publish content to a collection. One approach being investigated is to use a frictionless data package, with the package schema generated from the iSamples LinkML definitions.

Currently, four collections have content mapped to the common data model. Those data are exposed via an API that iSamples central uses to find changes and retrieve new and updated content. There is currently no mechanism in iSamples to add content to a collection - that is a role for each collection.

Each instance currently has the URL patterns:

BASE_URL/ui        Web user interface
        /docs      API documentation
        /          API operations base 

So for example, iSamples central currently has the base url of https://hyde.cyverse.org/isamples_central/ so the UI is accessible at:

https://hyde.cyverse.org/isamples_central/ui/

and the API docs are at:

https://hyde.cyverse.org/isamples_central/docs/

Current iSamples Central and iSamples-In-A-Box UI instances are at:

Each is a docker container instance that differ only in basic configuration properties. Deployment and upgrade is managed through Ansible playbooks to minimize operational overhead.

Basic use metrics are being recorded with a self hosted instance of plausible.io, available at

https://metrics.isample.xyz

There are several threads of UI prototyping activity exploring mechanims for selecting, navigating, and rendering large volumes of information accessible through iSample Central. Various prototypes are available at:

https://find.isample.xyz/