AnnBuilder and Diverse Mappings
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@johannes-graumann-2056
Last seen 8.1 years ago
Hello, I'm trying to build an annotation package for one of EBIs IPI data base using AnnBuilder. I'm trying to pull in the GO annotation unsing the mixed GenBank/RefSeq baseMapType, but the database is build from a very diverse set of sources and a significant number of entries has neither GenBank nor RefSeq IDs. The question to more advanced users is now: how would you proceed in this case? Is there a way to pull in Info using different baseMapTypes and than unify the outputs? Please advise, Joh
Annotation GO AnnBuilder Annotation GO AnnBuilder • 880 views
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@sean-davis-490
Last seen 5 weeks ago
United States
On Thursday 22 February 2007 12:00, Johannes Graumann wrote: > Hello, > > I'm trying to build an annotation package for one of EBIs IPI data base > using AnnBuilder. I'm trying to pull in the GO annotation unsing the mixed > GenBank/RefSeq baseMapType, but the database is build from a very diverse > set of sources and a significant number of entries has neither GenBank nor > RefSeq IDs. The question to more advanced users is now: how would you > proceed in this case? Is there a way to pull in Info using different > baseMapTypes and than unify the outputs? I think ultimately everything is mapped by AnnBuilder to an Entrez Gene ID, so if you can supply your own mapping to Entrez Gene ID from these various sources, that will probably suffice. Many data sources provide such a mapping. Sean
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
Hi, Johannes, You said "a significant number of entries has neither GenBank nor RefSeq IDs". Is there any other database identifiers associted with those entries? thanks nianhua
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 8.1 years ago
> >Total Entires: 52735 Unique Protein Index > >AnnBuilder usable(?; I didn't find a suitable baseMapTyype for Entrez >despite the post mentioning it) mappings: > 47787 Entrez Gene Number > 24414 GenBank > 32158 RefSeq > 39079 unigene > >Further there are Swiss-Prot, TrEMBL, Ensembl, UNIPARC and Vega mapping - >all for a subset ... I would map everything to Entrez Gene id and then use the mapping as the base file for ABPkgBuilder to build the annotation. > >How would you do it? > >Joh > >Johannes Graumann wrote: > >> Hello, >> >> I'm trying to build an annotation package for one of EBIs IPI data base >> using AnnBuilder. I'm trying to pull in the GO annotation unsing the mixed >> GenBank/RefSeq baseMapType, but the database is build from a very diverse >> set of sources and a significant number of entries has neither GenBank nor >> RefSeq IDs. The question to more advanced users is now: how would you >> proceed in this case? Is there a way to pull in Info using different >> baseMapTypes and than unify the outputs? >> >> Please advise, >> >> Joh >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 8.1 years ago
>But what's the right baseMapType for Entrez entries? The documentation reads: ll > >>baseMapType: 'baseMapType' a character string that is either "gb","ug", >> "image", "ll", "image", "refseq", "gbNRef" to indicate >> whether the probe ids in baseName are mapped to GenBack >> accession numbers, UniGene ids, image clone ids, LocusLink >> ids, RefSeq ids, or a mixture of GenBank accession numbers >> and RefSeq ids > >No mentioning of Entrez anywhere ... or does it correspond to genbank? > >Joh Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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@johannes-graumann-2056
Last seen 8.1 years ago
So here's the entire dilemma: Total Entires: 52735 Unique Protein Index AnnBuilder usable(?; I didn't find a suitable baseMapTyype for Entrez despite the post mentioning it) mappings: 47787 Entrez Gene Number 24414 GenBank 32158 RefSeq 39079 unigene Further there are Swiss-Prot, TrEMBL, Ensembl, UNIPARC and Vega mapping - all for a subset ... How would you do it? Joh Johannes Graumann wrote: > Hello, > > I'm trying to build an annotation package for one of EBIs IPI data base > using AnnBuilder. I'm trying to pull in the GO annotation unsing the mixed > GenBank/RefSeq baseMapType, but the database is build from a very diverse > set of sources and a significant number of entries has neither GenBank nor > RefSeq IDs. The question to more advanced users is now: how would you > proceed in this case? Is there a way to pull in Info using different > baseMapTypes and than unify the outputs? > > Please advise, > > Joh > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
Hi, Have you try biomaRt? Both IPI and BioMart are from EBI. I guess BioMart should provide better (more curated) cross-references between IPI accessions and other databases including GO. If you only need GO annotations, then biomaRt maybe a better choice. best nianhua
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