Taxonomic name is always empty

[laughedelic]

I need to check how it works with just the NCBITaxonomy Bio4j distribution.

[laughedelic]

Looking at the relevant Bio4j code, I don't see that the name property is set. And even in bio4j-titan the property type is not created.

Why the scientific name is empty as well, I don't understand.

@eparejatobes WDYT?

[laughedelic]

Solving in https://github.com/bio4j/bio4j/pull/103 and https://github.com/bio4j/bio4j-titan/pull/75

[laughedelic]

Reimported NCBITaxonomy (on m3.large):

Statistics for program ImportNCBITaxonomy:
Input file: nodes.dmp
There were 1426530 taxonomic units inserted.
The elapsed time was: 0h 7m 53s

And tested it on some random ids:

> import com.thinkaurelius.titan.core, com.bio4j.titan.model.ncbiTaxonomy._, com.bio4j.titan.util.DefaultTitanGraph
> val taxGraph: TitanNCBITaxonomyGraph = new TitanNCBITaxonomyGraph( new DefaultTitanGraph(core.TitanFactory.open("berkeleyje:/home/ec2-user/bio4j/") ) )
> def getName(id: Int): String = taxGraph.nCBITaxonIdIndex.getVertex(id.toString).get.name

> getName(2)
res2: String = Bacteria

> getName(54)
res3: String = Nannocystis exedens

> getName(132)
res4: String = Tuberoidobacter mutans

The database is uploaded to s3://resources.ohnosequences.com/16s/bio4j-taxonomy/ (the old one is in 16s/bio4j/)

[eparejatobes]

:clap: :clap: :clap:

[laughedelic]

:shipit:

[marina-manrique]

:tada: :dancer: