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knowledgesystems / pipelines-scrum

Repository for tracking uncategorizable issues related to backend pipelines work
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decide : change the base URI for concepts? #1291

Closed sheridancbio closed 1 month ago

sheridancbio commented 2 months ago

Done Condition (What do we need? Why do we need it? Keep this is small as possible!)

We have chosen the base URI for all oncotree concepts

Technical Description (How are we going to achieve the above)

The current base URI for our concepts begins with "http://data.mskcc.org" ... but this server does not exist. We imagine that "publication" of schemes/concepts may require a true web server at this URI which can "receive" concept definitions (via HTTP POST). We should learn more about publication and consult with the graphite representatives.

Potential Issues

Dependencies

Technical Requirements

Outside People/Teams

Changes

sheridancbio commented 1 month ago

The concern here was whether or not we needed to adjust the base URI to accommodate the graphite "publish" operation (which we did not understand). After reading documentation and doing webpage searches, our best understanding is that the base URI is not determined by any destination server.

The most informative webpage was this one: https://www.synaptica.com/publishing/ which describes publishing as a combination of pull (via api) and push (via adaptor plugin) functionalities which allow the connection of diverse client systems (called content management systems, such as confluence and sharepoint)

Based on this the only essential thing about the base URI is that it distinguish the defined concepts from all other concepts in the ontology management system. We can continue to use our root URI http://data.mskcc.org with all oncotree concepts living under URI http://data.mskcc.org/ontologies/oncotree. The other base URI we used for oncotree was for holding OncotreeVersionList concepts. That used base URI http://data.mskcc.org/taxonomies/OncoTreeVersionList but I believe it would be best to convert these concepts to use the same base URI as the regular oncotree nodes rather than having a separate base URI.