idali0226 / information-model

Discussions about the information model and ideas about changes

This space captures discussions about the information model and ideas about changes. Please add your materials to this repo!

Exposing the Information Model through Web APIs

Module map - high level system overview

The modules.odg is of historical interest as a high level map over some important data types and services in the DINA system....

Important data types and services

  Some core data types     Some associations to other data types
  (NOUNS)
 +-----------------------+
 |  CollectionObject     | incl "containers" and links to media, projects
 +-----------------------+ catalogues, collection, determinations etc
 +-----------------------+
 |   Taxon / taxonomy    | determinations, links to most other data types
 +-----------------------+
 +-----------------------+
 |  Locality / places    | links to geography, collecting events, ref works,
 +-----------------------+ habitat, stratigraphy
 +-----------------------+
 |  Storage location     | space (time?) coord for physical storage location
 +-----------------------+
 +-----------------------+
 |   User/Agent/People   | incl org/group links, generates events such as
 +-----------------------+ determinations, accessions, loans etc
 +-----------------------+
 |  Reference work       | citations
 +-----------------------+
 +-----------------------+
 |  Media (binary assets)| depictions, sounds and other associated objects
 +-----------------------+

 Higher level web APIs expose functionality needed for compound tasks, such as
   - reporting / statistics / printing etiquettes etc
   - "workbench" type functionality for migrating data in and out
   - managing collections including loans, data entry etc

 Web UI components provide clients or front-end to support these tasks
 interactively and while doing so work against backend web APIs.
 +-----------------------+
 |   DNA (LIMS seqs etc) |
 +-----------------------+
 +-----------------------+
 |   Species Profile     | links text and images to a taxon,
 +-----------------------+ describes habitat, behaviour etc

# Text diagrams can be created with JavE
# src: http://www.jave.de/download/download.html 
# cmd: java -jar jave5.jar

Web UIs versus Web APIs - overview of DINA architecture

   FRONT-ENDS / CLIENTS / WEB UIs

   +------------------+ +---------------+ +-----------------+ +----------------+
   |Coll Data Entry XL| |Species Profile| |DNA Seq Mgm      | |Loans from Coll |
   +------------------+ +---------------+ +-----------------+ +----------------+
   +-------------------+ +--------------------+  +---------+  +----------------+
   |Geological Coll Mgm| |Search UI for Colls |  |Support  |  |Loans Mgm       |
   +-------------------+ +--------------------+  +---------+  +----------------+
                        +-----------------------+
    The UIs above       | General Collections   |
    exist but not ->    | Mangament Web UI      |
                        +-----------------------+

  ----------------------------DINA Web APIs--------------------------------------

  BACK-ENDS / SERVERS / WEB APIs

  +-------------+  +-------------+ +----------+ +-------------+  +-------------+
  |Taxonomy API |  |DNA Seq API  | | SPM API  | |Coll Mgm API |  |Media API    |
  +-------------+  +-------------+ +----------+ +-------------+  +-------------+

  The APIs       +---------+  +-------------+  +-------------+   +--------------+
 above exist     |User API |  |Locality API |  |Storage API  |   | Batch IO API |
but not these -> +---------+  +-------------+  +-------------+   +--------------+

Current Web UIs / clients / front-ends

The following UI components are currently available and make use of the backend web APIs:

• Species Information

• Public Loans from Collections

• Managing Loans in Collections

• Batch Data Entry into Collections through Excel

• Linking data to Collections using DNA

• Searching across Collections

• Operational Support (Tickets etc) for DINA-Web

Current Web APIs / servers / back-ends

Existing modules and their respective doucumented web APIs:

• Taxonomy management
• [DNA data web APIs from seqdb](no online docs yet) DOCS IN PROGRESS
• Species Profile Model API in The Naturalist
• Media API DOCS IN PROGRESS
• [DINA Specify REST API](no online docs yet) DOCS IN PROGRESS
• [Dina Data Tool](no online docs yet) DOCS IN PROGRESS

Current CLI Tools

• CollectionBatchTool

Guidelines and principles of construction

Here are information about various guidelines and principles of construction that inspire and guide the construction, design and future development of DINA-Web:

• Functional guidelines - API design guidelines
• Style guidelines - Visual design guidelines
• Licensing guidelines
• Data exchange guidelines - Import and export of data

System diagram for DINA-Web components

DINA-Web infrastructure

Please see Infrastructure for an overview of the technology stack that the DINA system runs on.