Frequently Asked Questions (FAQ)
These are the most frequently asked questions (FAQ) at the GO Helpdesk. You may find the answers to all of your questions here. If not, feel free to contact the Helpdesk by clicking on the "Contact" link in the main menu.
amigo (9)
Questions and answers that have to do with AmiGO specifically.
- How do I browse the GO?
- What data does AmiGO use? Are there IEAs? If so, which ones?
- How do I find manually annotated gene products only, i.e. how do I sort by evidence code?
- What are the recommended data access policies for your services?
- What is the best way to link into AmiGO?
- How do I install AmiGO locally?
- What are the differences between the data available in AmiGO and those on QuickGO?
- How can I do term enrichment analysis for a species that is not present in the list from AmiGO?
- Where can I find the number of terms in each of the ontologies?
analysis (8)
Topics including things like subsets (slimming) and enrichment analysis.
- Can a single gene product be annotated with more than one GO term?
- How can I programmatically get a list of GO terms associated with a gene identifier?
- How can I do term enrichment analysis for a species that is not present in the list from AmiGO?
- How do I annotate a de novo assembled transcriptome against the GO database?
- Does the Term Enrichment tool have a limit on the number genes in the input file?
- How do I use GO's Term Enrichment tool?
- How do I map a set of annotations to high level GO terms (GO slim)?
- What is the minimum information to include in a functional analysis paper?
annotation (33)
Annotation related questions (e.g. evidence codes, ID mapping...).
- How are binary interactions curated by the IntAct group selected for export to GO as protein binding (GO:0005515) annotations?
- Can a single gene product be annotated with more than one GO term?
- How can I programmatically get a list of GO terms associated with a gene identifier?
- What are the differences between the data available in AmiGO and those on QuickGO?
- What is the best way to obtain the GO annotations for a list of Ensembl IDs in batch?
- How do I access older versions of gene association files?
- How can I do term enrichment analysis for a species that is not present in the list from AmiGO?
- How do I find all annotations for species X that I can't find in AmiGO?
- How do I annotate a de novo assembled transcriptome against the GO database?
- What is the difference between the filtered and unfiltered versions of the GOA UniProt gene associations files?
- How do I map a set of annotations to high level GO terms (GO slim)?
- How can I contribute to GO?
- How do I submit annotations to GO?
- Where can I find software to allow me to browse the GO terms and annotations?
- How do I annotate ESTs?
- How often does automatic annotation give results that are consistent with manual annotation?
- How is annotation quality controlled to ensure consistency between databases?
- What are the advantages and disadvantages of automatic annotation?
- What are the advantages and disadvantages of manual annotation?
- Why are some gene products annotated to both a parent term and a child term?
- Can a gene or gene product be annotated to more than one term from an ontology?
- What is an evidence code?
- What criteria are used to annotate genes with GO terms?
- How are gene products associated with GO terms?
- What is a 'gene product'?
- What is annotation?
- How is the GO used in genome analysis?
- Where can I find GO annotations of proteins and ESTs?
- What gene or protein IDs should I use?
- What is the best way to obtain the GO annotations for a list of UniProt Accession Numbers in batch?
- Where can I find software to allow me to make or edit GO annotations?
- Where can I view or download the complete sets of GO annotations?
- Sometimes the number of GO annotations changes significantly over a short period of time. Why?
consortium (3)
Questions and answers about the Consortium itself.
database (8)
Questions and answers concerning the legacy Gene Ontology MySQL database.
- How do I annotate a de novo assembled transcriptome against the GO database?
- What are the recommended data access policies for your services?
- What is the best way to obtain the GO annotations for a list of UniProt Accession Numbers in batch?
- I want to use the database files but...
- Why do the IDs in the database not match the GO IDs?
- How do I find terms, annotations, or gene products in the database?
- How do I query, access, install/mirror the GO database?
- What is the status of the GO MySQL database?
downloads (5)
Questions and answers about downloads: what they are and where to get them.
- What is the best way to obtain the GO annotations for a list of Ensembl IDs in batch?
- How do I access older versions of gene association files?
- How do I find all annotations for species X that I can't find in AmiGO?
- What is the difference between the filtered and unfiltered versions of the GOA UniProt gene associations files?
- What is the best way to obtain the GO annotations for a list of UniProt Accession Numbers in batch?
errors and bugs (1)
Questions related to various errors and bugs.
format (10)
These are questions and answers about the various file formats that can be found with the Gene Ontology Consortium.
- What is a GPI file?
- What is OBO file format?
- What gene or protein IDs should I use?
- Why are the ontologies initially produced in OBO flat file format instead of XML?
- Why won't the RDF-XML file parse using RDF parsers?
- How can I generate files in the old GO flat file format?
- What is an OWL file?
- What are the file formats used by the Gene Ontology?
- What is a GPAD file?
- What is a GAF file?
general (18)
General questions about the Gene Ontology.
- What is the GO?
- Why do we need GO?
- Which biological domains are supported by GO?
- Where can I view or download the complete sets of GO annotations?
- Sometimes the number of GO annotations changes significantly over a short period of time. Why?
- What is beyond the scope of the GO project?
- Can I reason over GO?
- I want to use GO, but I don't know where to begin
- How can I contribute to GO?
- Where can I find software to allow me to browse the GO terms and annotations?
- What is the minimum information to include in a functional analysis paper?
- I have a question about gene or protein nomenclature
- What are all the possible uses of GO?
- How is the GO used in genome analysis?
- Where can I find GO annotations of proteins and ESTs?
- How do I cite the GO?
- What am I allowed to do with the data?
- How do I browse the GO?
mappings (4)
Questions and answers about mappings: the translation of one type of ID into another.
ontology (18)
Ontology related questions (e.g. structure, relations, subsets/slims...).
- How can I contribute to GO?
- How can I suggest new GO terms?
- What is beyond the scope of the GO project?
- Can I reason over GO?
- Can a single gene product be annotated with more than one GO term?
- How can I programmatically get a list of GO terms associated with a gene identifier?
- How do I get the term names for my list of GO ids?
- Where can I find the number of terms in each of the ontologies?
- How do I map a set of annotations to high level GO terms (GO slim)?
- Where can I find software to allow me to edit the GO terms?
- Can I download the ontologies as an Excel spreadsheet?
- How can I calculate the "level" of a GO term?
- Where have the 'unknown' terms gone?
- Does the GO ID have any meaning?
- Can a term in one ontology have parents in one of the other two ontologies?
- Can a term that is listed in two places in an ontology file have children in one place but not in the other?
- What is an ontology?
- What is GO "content"?
other (3)
Other general questions about the Gene Ontology and its products.
participation (2)
Questions and answers related in participation in the GO community.
software (23)
Software related questions (e.g. AmiGO, OBO-Edit, database, scripts, OWL, file formats...).
- How can I do term enrichment analysis for a species that is not present in the list from AmiGO?
- How do I find all annotations for species X that I can't find in AmiGO?
- How do I map a set of annotations to high level GO terms (GO slim)?
- Where can I find software to allow me to browse the GO terms and annotations?
- What is a GPI file?
- What is the best way to link into AmiGO?
- What is OBO file format?
- Why are the ontologies initially produced in OBO flat file format instead of XML?
- Why won't the RDF-XML file parse using RDF parsers?
- How can I generate files in the old GO flat file format?
- What are the recommended data access policies for your services?
- What is an OWL file?
- What are the file formats used by the Gene Ontology?
- What is a GPAD file?
- What is a GAF file?
- I want to use the database files but...
- Why do the IDs in the database not match the GO IDs?
- How do I find terms, annotations, or gene products in the database?
- How do I query, access, install/mirror the GO database?
- Where can I find software to allow me to make or edit GO annotations?
- What is the status of the GO MySQL database?
- Where can I find software to allow me to edit the GO terms?
- How do I install AmiGO locally?
submission (2)
Questions and answers related to the submission of data to the Gene Ontology Consortium.
third-party tools (4)
Questions related to third-party tools (not AmiGO, OBO-Edit, etc.).
- How can I programmatically get a list of GO terms associated with a gene identifier?
- How can I do term enrichment analysis for a species that is not present in the list from AmiGO?
- How do I find all annotations for species X that I can't find in AmiGO?
- How do I annotate a de novo assembled transcriptome against the GO database?