Latest revision as of 10:40, 12 August 2019

Overview

This page describes the status of the public Solr index for the GO. This index will replace some of the query functionality for GOOSE as well as become the new backend for AmiGO 2 and other services. A preview server is now active at http://golr.berkeleybop.org.

Public beta

The preview server at http://golr.berkeleybop.org is currently in beta.

Some preview documentation is at http://cdn.berkeleybop.org/jsapi/bbop-js/docs/index.html

Use

Feel free to use it as you will and start to write for it. As this is still a little early, we are only loading the GO, CL, ECO, and taxslim, as well as non-IEA annotations from the GAFs. Please see the AmiGO_Labs caveats, as well as the downtime information on this page.

Implementation progress

We are now loading properly from owltools.

We have looked at nginx as a reverse proxy for speed and to prevent unauthorized access to non-select URLs on the Solr server, and found it to be good.

The GOlr server is now active at http://golr.berkeleybop.org (nginx front on stove).

We now also have http://amigo2.berkeleybop.org working on stove and backed by golr.berkeleybop.org.

We are now on Solr 3.6.

Schema progress

We are currently working towards a flexible schema as defined in the owltools code. As we roll it out for the AmiGO backend and as a replacement for common GOOSE queries, we expect to find holes in the schema, documented below.

Currently, the index is entirely populated by through an owltools command line program, using YAML files for configuration. For more information, see the Installation section below.

Query examples for the GOlr Schema

Example queries on the wiki.

Some old queries require the use of Solr facets and some modification of code Seth has written to present simpler results queries (i.e. the facet results are not displayed).
Note: hierarchical queries that 'combine' facet queries can be handled by the facet.pivot functionality that is available in Solr 4. In the meantime, we'll see if we can devise a work-around.

Current holes in the GOlr schema

None listed at this time...

Downtime

Now that we have entered beta, downtimes are sporactic as we work with the software stack. As we approach production, the automatic update times will be decided and posted.

Local installation (data and schema development)

GOlr installation information and Solr installation help can be found here.

Collaborations

In order to make a truly useful system for the community at large, the Gene Ontology Consortium is working directly with other groups on GOlr tools, schema, and library development.

Virtual Fly Brain (VFB)

We're working with VFB on schema and ontology tools development to help enable rich ontology interaction and search at speed. This will also help push the envelope on the types of use cases that we might see.

@@ Line 1: / Line 1: @@
+[[Category:Software]]
+[[Category:GOlr]]
 =Overview=
-This page describes the status of the public Solr index for the GO. This index will replace some of the query functionality for GOOSE as well as become the new backend for AmiGO and other services. A preview server is now active at http://golr.berkeleybop.org.
+This page describes the status of the public Solr index for the GO. This index will replace some of the query functionality for GOOSE as well as become the new backend for AmiGO 2 and other services. A preview server is now active at http://golr.berkeleybop.org.
-=Use=
+=Public beta=
+The preview server at http://golr.berkeleybop.org is currently in beta.
+Some preview documentation is at http://cdn.berkeleybop.org/jsapi/bbop-js/docs/index.html
+==Use==
 Feel free to use it as you will and start to write for it. As this is
-still a little early, we are only loading the GO, CL, and taxslim, as well as the
+still a little early, we are only loading the GO, CL, ECO, and taxslim, as well as non-IEA annotations from the GAFs. Please see the [[AmiGO_Labs]] caveats, as well as the [[#Downtime | downtime]] information on this page.
-MGI and dictyBase GAFs. Please see the [[AmiGO_Labs]] caveats, as well as the [[#Downtime | downtime]] information on this page.
-=Implementation Progress=
+==Implementation progress==
 We are now loading properly from [https://code.google.com/p/owltools/ owltools].
@@ Line 21: / Line 28: @@
 We are now on Solr 3.6.
-=Schema Progress=
+==Schema progress==
 We are currently working towards a flexible schema as [http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/gold/solr/conf/schema.xml?revision=4429&content-type=text%2Fplain defined] in the owltools code. As we roll it out for the AmiGO backend and as a replacement for common GOOSE queries, we expect to find holes in the schema, documented below.
-Currently, the index is entirely populated by through an owltools command line program, using [https://code.google.com/p/owltools/source/browse/#svn%2Ftrunk%2FOWLTools-Solr%2Fsrc%2Fmain%2Fresources YAML] files for configuration. The Solr schema.xml generation looks like:
+Currently, the index is entirely populated by through an owltools command line program, using [https://code.google.com/p/owltools/source/browse/#svn%2Ftrunk%2FOWLTools-Solr%2Fsrc%2Fmain%2Fresources YAML] files for configuration. For more information, see the ''Installation'' section below.
- owltools --solr-config /home/sjcarbon/local/src/svn/owltools/OWLTools-Solr/src/main/resources/ont-config.yaml /home/sjcarbon/local/src/svn/owltools/OWLTools-Solr/src/main/resources/bio-config.yaml /home/sjcarbon/local/src/svn/owltools/OWLTools-Solr/src/main/resources/ann-config.yaml /home/sjcarbon/local/src/svn/owltools/OWLTools-Solr/src/main/resources/ann_ev_agg-config.yaml --solr-schema-dump
-With the actual population along the lines of:
- owltools http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl http://purl.obolibrary.org/obo/cl.owl http://purl.obolibrary.org/obo/go.owl http://purl.obolibrary.org/obo/eco.owl --solr-url http://localhost:8080/solr/ --solr-purge --solr-config /home/bbop/local/src/svn/owltools/OWLTools-Solr/src/main/resources/ont-config.yaml --solr-load-ontology --solr-load-gafs /srv/tmp/gene_association.mgi
+==Query examples for the GOlr Schema==
-==Rewriting old GOOSE query examples for the new GOlr Schema==
 Example queries on the [http://wiki.geneontology.org/index.php/Example_Solr_Queries wiki].
@@ Line 40: / Line 41: @@
 * Note: hierarchical queries that 'combine' facet queries can be handled by the facet.pivot functionality that is available in Solr 4. In the meantime, we'll see if we can devise a work-around.
-==Current Issues and Problems with the GOlr Schema==
+== Current holes in the GOlr schema ==
-* No PANTHER data
+* None listed at this time...
-** <strike>We'll look at creating a new document type from Suzi's PAINT code.</strike>
-** Looking to add PANTHER data as extra fields.
-* A few suggestions to make use of the document categories easier:
+== Downtime ==
-** <strike>bioentity 'source' was not loaded correctly in the version I was testing</strike> FIXED
-** <strike>annotation should have 'with' field (I believe Seth said this is coming but thought I'd get it written down here)</strike> FIXED
-** <strike>ontology_class should have 'synonyms' and 'closure' (I believe Seth said this is coming)</strike> should be in now
-** <strike>annotation_aggregate should have 'go_id' as a separate field (I believe Seth said this is coming as 'alternate_id')</strike> should be annotation_class* (fixed)
-** <strike>all id/label closure pairs need a corresponding JSON structure to map the two to eachother</strike>
-** <strike>JSON blob for graph structure</strike>
-= Downtime =
+Now that we have entered beta, downtimes are sporactic as we work with the software stack. As we approach production, the automatic update times will be decided and posted.
-Rebuilds start at 10pm PDT (6am BST; 5pm NZST), so there may be some data gaps in there, but that is most significant for document types other than ontology_class (which get rebuilt rather quickly).
+= Local installation (data and schema development) =
-At the time of this writing, this process is taking under an hour.
+GOlr installation information and Solr installation help can be found [[GOlr:_Installation | here]].
+=Collaborations=
-[[Category:SWUG Projects]]
+In order to make a truly useful system for the community at large, the Gene Ontology Consortium is working directly with other groups on GOlr tools, schema, and library development.
-[[Category:Software]]
-[[Category:AmiGO]]
+==Virtual Fly Brain (VFB)==
-[[Category:Software Progress]]
-[[Category:Seth]]
+We're working with [http://www.virtualflybrain.org VFB] on schema and ontology tools development to help enable rich ontology interaction and search at speed. This will also help push the envelope on the types of use cases that we might see.
-[[Category:Mary]]

GOlr: Difference between revisions