Hey,
I was using DAVID (http://david.abcc.ncifcrf.gov/conversion.jsp) to do the gene ID conversion, e.g.conversion between Agilent ID, Genebank accession id and Entrez gene ID, but I found the DAVID database is not updated. Does anyone know a better updated conversion tool to do this job? Thanks!
The bioDBnet and Hyperlink Management System (HMS) systems convert multiple ID sets to each other.
HMS is limited to three species (human, mouse ciona) and has fewer data sources (Agilent - no, GenBank and Entrez - yes).
The bioDBnet system appears to be species-neutral and the network of linked databases is shown here, (includes Agilent, GenBank and Entrez, so it should fit your requirements):
MyGene.info is a web service that provides up to date annotations in several fields and is great for gene ID conversion. All species from NCBI and Ensembl are supported and annotations are updated weekly to ensure the latest annotations are available. Both python and R/Bioconductor clients are easy to use.
MyGene.info may not be able to solve your problem with Agilent IDs but several other IDs from Genebank, Uniprot, Ensembl, Refseq are all available. Also, from either client, you can query several thousand genes at once.
Here is some example syntax for ID conversion from the python module:
>>> import mygene
>>> mg = mygene.MyGeneInfo()
>>> mg.metadata['available_fields'] ## returns available query terms, pay special attention to "ensemblgene", "entrezgene", "symbol" and "uniprot"
[u'accession', u'alias', u'biocarta', u'chr', u'end', u'ensemblgene', u'ensemblprotein', u'ensembltranscript', u'entrezgene', u'exons', u'flybase', u'generif', u'go', u'hgnc', u'homologene', u'hprd', u'humancyc', u'interpro', u'ipi', u'kegg', u'mgi', u'mim', u'mirbase', u'mousecyc', u'name', u'netpath', u'pdb', u'pfam', u'pharmgkb', u'pid', u'pir', u'prosite', u'ratmap', u'reactome', u'reagent', u'refseq', u'reporter', u'retired', u'rgd', u'smpdb', u'start', u'strand', u'summary', u'symbol', u'tair', u'taxid', u'type_of_gene', u'unigene', u'uniprot', u'wikipathways', u'wormbase', u'xenbase', u'yeastcyc', u'zfin']
>>> xli = ['DDX26B','CCDC83', 'MAST3', 'RPL11', 'ZDHHC20', 'LUC7L3', 'SNORD49A', 'CTSH', 'ACOT8']
>>> mg.querymany(xli, scopes="symbol", fields=["uniprot", "ensembl.gene", "reporter"], species="human", as_dataframe=True)
A DataFrame is returned:
And now for the Bioconductor package:
library(mygene)
xli <- c('DDX26B','CCDC83', 'MAST3', 'RPL11', 'ZDHHC20', 'LUC7L3', 'SNORD49A', 'CTSH', 'ACOT8')
queryMany(xli, scopes="symbol", fields=c("uniprot", "ensembl.gene", "reporter"), species="human")
This returns a DataFrame:
Finished
DataFrame with 9 rows and 5 columns
ensembl.gene _id uniprot.Swiss-Prot uniprot.TrEMBL query
<CharacterList> <character> <character> <List> <character>
1 ENSG00000165359 203522 Q5JSJ4 ######## DDX26B
2 ENSG00000150676 220047 Q8IWF9 ######## CCDC83
3 ENSG00000099308 23031 O60307 ######## MAST3
4 ENSG00000142676 6135 P62913 ######## RPL11
5 ENSG00000180776 253832 Q5W0Z9 ######## ZDHHC20
6 ENSG00000108848 51747 O95232 ######## LUC7L3
7 ENSG00000277370,ENSG00000175061 26800 NA ######## SNORD49A
8 ENSG00000103811 1512 P09668 ######## CTSH
9 ENSG00000101473 10005 O14734 ######## ACOT8
There is already a request for including Agilent reporter IDs in MyGene.info:
https://bitbucket.org/sulab/mygene.info/issue/1/support-for-agilent-platform-reporters
Please leave a comment there if someone need any specific platforms to be included.
Hi,
I am converting the gene IDs of apple, e.g., MDP0000006982, MDP0000007682, MDP0000799306,MDP0000799753, into entrez ID and ensemble gene ID using R bioconductor package "mygene", but function "queryMany" has not been working and giving error continuously.
Does anyone help me how to convert these IDs, please suggest any suitable tool or how to fix the above-mentioned issue?
Thanks
BioMart has already been mentioned. It can do much more than ID conversion but it is very useful for conversion purposes, it is regularly updated and you can select different genome builds and all kinds of genomic features. It seems to me that you wish to retrieve GeneIDs linked to Affymetrix IDs. To select these attributes in BioMart: go to the Martview page to start a new BioMart query.
Select attributes on the attribute page: The Ensembl GeneIDs and Transcript IDs are default. Ensembl GeneID and Affy IDs are under the "External" tab. Select your chip there. To limit to those genes which are on the chip, use the Filters->Gene menue. You can limit the genes to those present on various platforms or your favourite set.
There is an URL button in biomart that allows to retrieve a URL for your query and to pass it on to others. Try this example:
BioMart URL URL, that should be a good starting point.
If you are interested in KEGG identifiers (Pathways, Genes), EC-numbers, etc. the
KEGG Identifier page could be handy, because the KEGG ids are not in BioMart as far as I know.
BridgeDB is really a software framework that you can use in our own code; either directly (currently only in Java) or through calling it as a webservice. It can use different and even multiple stacked mappings. By default these come from ENSEMBL (for gene products) and HMDB (for metabolites). Ongoing projects extend the available mappings with ChemSPider and SNP info. There is a short introduction available at Nature Precedings: http://precedings.nature.com/documents/5023/version/1 and a paper in BMC Bioinformatics: http://dx.doi.org/10.1186/1471-2105-11-5
You can also do it with the following services:
If you have just a few, I just saw someone use the R package BioIDMapper and it seemed kind of neat. But it's slow.
There is a more recent version at: http://sourceforge.net/projects/bioidmapper/
The following link has a list of ID conversion tools:
http://idconverter.bioinfo.cnio.es/
Is another possible solution to this, although you might find this is not as up to date as you might like either.
Try out: http://mygene.info/v2/api#MyGene.info-gene-query-service
It's Awesome!
Have a look at the (BETA stage) Ensembl REST API
For example, for converting from Ensembl Gene ids to Gene symbols, you could use a query like this one:
http://beta.rest.ensembl.org/xrefs/id/ENSG00000059804?content-type=application/json
... and then programmatically (some python parsing should be rather straight forward) extract the "display_id" for the items that have "dbname" = "HGNC", or "EntrezGene".
For example, the following PHP code did the trick for me:
# Test the new Ensemble REST API with an example gene
$ensemblID = "ENSG00000157764";
$url = "http://beta.rest.ensembl.org/xrefs/id/$ensemblID?content-type=application/json";
$ensemblResultJson = file_get_contents($url);
$ensemblResult = json_decode($ensemblResultJson, true);
# Print out each found Gene symbol on a separate row:
echo "<ul>";
foreach ($ensemblResult as $mapping) {
if ( in_array( $mapping['dbname'], array("EntrezGene","HGNC"))) {
echo "<li>Found Gene symbol: " . $mapping['display_id'] . "</li>\n";
}
}
echo "</ul>";
The most easy way is as the follow:
GeneID convert:
http://www.ensembl.org/biomart/martview
I don't know of a direct solution myself, but this is a topic that may be of interest for the biological data analysis class that I am teaching.
If you specify the organism/genomic builds that you are interested in we may be able to generate a full translation list as an in class example or a homework. I was planning on covering an Affymetrix ID to Genebank example anyhow.
Not sure what your background is, however, we recently started to develop an id mapper / converter for experimentalists who prefer organizing their data in Excel. Therefore, the client directly integrates into MS Excel.
Currently, we provide the possibility to map from various IDs to ensembl and back. The mapping data were extracted from Ensembl 73 (released on the 4.9.2013). If you need mappings for any additional ID types availalble from the ensembl database we will be happy to add them (please just tell us via our feedback form).
I don't really understand the need for this. Many identity mappers offer webservices and if needed these can be installed locally. That is definitely true for our own BridgeDb. Is there any reason you could not just call these services from Excel? (And yes that would allow mapping from ENSEML gene ID to HGNC or from probeset IDs)
Share a R script to do it:
library("org.Hs.eg.db")
symbol <- as.list(org.Hs.egALIAS2EG)
symbol2geneid<-data.frame(names(symbol),as.character(symbol))
BioDBnet is a great tool for database do database id conversion. Link is https://biodbnet-abcc.ncifcrf.gov/db/db2db.php
You can convert the gene id to a different different database like Agilent ID, GO ID, Pathway ID. You can check the link to see all the databases available.
I have used it to convert the Gene ID to GO ID.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
How frequently do you need things updated? DAVID does have yearly releases so far, but their latest release is this month (March 2010). See the release announcement here: http://david.abcc.ncifcrf.gov/forum/cgi-bin/ikonboard.cgi?act=ST;f=10;t=25 This does suggest the underlying mapping framework will be updated along with it in the 6.7 beta, and hence should include more recent information for the conversion tool
Hi
I am faced the same problem.I did differential gene expression by using this protocol "Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown"
I have gene list file after using the ballgown
the gene id in this files is as
I want to perform gene ontology next by using tool AgriGo. these gene ids are not recognized in any database.
I have use the tool bioDBnet to convert these ids into ensembl gene id .but not found result.
I would say that the suffix numbers are Entrez IDs (Gene IDs).