Linking in to your mine

This page aims to describe the various ways to link to a Mine.

Link directly to query results

Template name

Links to results of specified template. URL is generated on template form in webapp.

http://www.flymine.org/query/loadTemplate.do?name=Chromosome_Gene&constraint1=Gene.chromosome.primaryIdentifier&op1=eq&value1=2L&constraint2=Gene.organism.name&op2=eq&value2=Drosophila+melanogaster&method=results

Make sure to include &method=results at the end of the query string.

Query XML

Links to results of query. It can run any query built by QueryBuilder; QueryBuilder generates the XML.

http://www.flymine.org/query/loadQuery.do?skipBuilder=true&query=%0A%3Cquery+name%3D%22%22+model%3D%22genomic%22+view%3D%22Gene.primaryIdentifier+Gene.secondaryIdentifier+Gene.goAnnotation.ontologyTerm.name+Gene.goAnnotation.ontologyTerm.identifier+Gene.goAnnotation.ontologyTerm.namespace%22+sortOrder%3D%22Gene.primaryIdentifier+asc%22%3E%0A++%3Cconstraint+path%3D%22Gene.organism.shortName%22+op%3D%22%3D%22+value%3D%22A.+gambiae%22%2F%3E%0A%3C%2Fquery%3E%0A&trail=%7Cquery&method=xml

Link to List Analysis page

Template results

Links to list analysis page comprised of results of template query. "path" attribute determines which column is used to create list. URL is available on template form in webapp.

http://www.flymine.org/query/loadTemplate.do?name=Pathway_Genes&constraint1=Pathway.name&op1=eq&value1=Pentose+phosphate+pathway&constraint2=Pathway.genes.organism.name&op2=eq&value2=Drosophila+melanogaster&constraint3=Pathway.dataSets.name&op3=eq&value3=KEGG+pathways+data+set&method=list&path=Pathway.genes

List of Identifiers

Links to list analysis page for specified objects. For a very long list, use a form instead of a link. It can use any identifiers.

http://www.flymine.org/query/portal.do?externalids=CG2262,CG3069,CG2859,CG5041,FBgn0036513&class=Gene

Query builder

Links directly to query builder, starts a query using the provided list.

http://beta.flymine.org/beta/loadQuery.do?name=copy&method=list

Report page

Links directly to report page. URL available on report page in webapp.

http://www.humanmine.org/humanmine/portal.do?externalids=pparg&class=Gene&origin=readthedocs

Optionally, add extraVlue parameter with the organism name, e.g.:

http://www.humanmine.org/humanmine/portal.do?externalids=pparg&class=Gene&extraValue=H.+sapiens

Link into Mine with Orthologues

The example URL contains ''D. melanogaster'' genes. The results will contain the corresponding ''C. elegans'' genes, if any. This will only work if you have orthologue data loaded into your Mine. It will forward to report page OR list analysis page.

http://www.flymine.org/query/portal.do?externalids=CG2262,CG3069,CG2859,CG5041,FBgn0036513&class=Gene&orthologue=C.%20elegans

Convert any identifiers to Genes

When linking to a report page or a list analysis page you can convert the data type, for instance, if you provide a Protein identifier and want to link to the corresponding Gene, you need to specify the class as Gene. It will only work if you have a converter template available

http://www.flymine.org/query/portal.do?externalid=EVE_DROME&class=Gene

More examples

See FlyMine for more examples: https://intermineorg.wordpress.com/flymine/link-to-flymine/