An open knowledge graph for BioBricks.ai
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License: MIT License
An open knowledge graph for BioBricks.ai
License: MIT License
An open knowledge graph for BioBricks.ai
From the grant
In coordination with Theme 2, BioBricks-OKG will be built so that all data can be accessed using FAIR tools like SPARQL...In this deliverable a checklist will be designed for the integration of new data sources and the management of governance of every integrated source. Other proto-okn groups will be contacted to discover other best practices for source governance.
From the grant
In this deliverable a set of 6+ assets will be chosen to transform into local, isolated, knowledge graphs. Eventually every compatible BioBricks-AI asset will be added to the knowledge graph.
Let's go a step farther and actually create those local knowledge graphs.
Please prepare a 15-minute presentation covering the following:
Agency representatives as well as representatives from Themes 2 and 3 projects may be present during these review meetings.
Lower priority than #14.
From the grant
... A centralized testing and logging system like DataDog will be integrated into scripts that transform source data into knowledge graphs. Because the BioBricks system already stores versioned snapshots of each data asset, it is possible to maintain a stream of data asset updates and to revert to an older version when there is an error until a fix can be implemented. Insilica developers will be deployed to address these issues as they occur.
Our local knowledge graph creation process should:
From the grant
Ontology alignment methods will be reviewed, proposed, and preliminary testing completed to automate the recognition of equivalent classes between knowledge graphs and synchronize them to the core graph.
It is a good idea to start exploring these before implementing too many of the local knowledge graphs in #1 as harmonization methods may inform ontology creation #2 and local knowledge graph constraints #1
https://github.com/biobricks-ai/biobricks-okg/blob/main/report/2024-01-15/graph-names.rq
This query gives me an error.
Virtuoso 37000 Error SP031: SPARQL compiler: The list of return values contains '*' but the pattern does not contain variables
SPARQL query:
define sql:big-data-const 0
#output-format:text/html
define sql:signal-void-variables 1
SELECT DISTINCT ?g_prefix
WHERE {
GRAPH ?g { }
BIND( URI(STRBEFORE(STR(?g), '?file=')) AS ?g_prefix )
}
ORDER BY ?g_prefix
If I update the query to the below I get a timeout. Is there no efficient way to get the graph names in our graph?
Virtuoso 42000 Error The estimated execution time 9360 (sec) exceeds the limit of 400 (sec).
SPARQL query:
SELECT DISTINCT ?g_prefix
WHERE {
GRAPH ?g { ?s ?p ?o }
BIND( URI(STRBEFORE(STR(?g), '?file=')) AS ?g_prefix )
}
ORDER BY ?g_prefix
From the grant
This task will form the core schema on which ontology alignment methods expand. A class to track data sources will be implemented to enable data provenance tracking.
A presentation of completed alpha deliverables will be given and a system to add sources to the
Open Knowledge Graph is complete with entities from multiple sources already added.
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