- FAQs about AspGD
- Why hasn't AspGD cited my paper?
- How do I propose a gene name?
- How can I find more information about the AspGD sequences?
- How should I cite AspGD?
- How can I get more help?
- FAQs about Gene Ontology at AspGD
- What is Gene Ontology (GO)?
- How do I find which genes or proteins are annotated to a GO term?
- How can I analyze the GO terms assigned to a set of genes?
- How does AspGD assign references for GO terms?
- FAQs about A. nidulans
We aim to collect all the available literature for each gene or protein of the species that we curate (currently Aspergillus nidulans and A. fumigatus). If your paper is not listed in AspGD, it was not intentionally excluded. AspGD curation is in progress, and we have not yet read every paper on our list, so your paper may be awaiting curation. The possibility also exists that your paper was accidentally omitted from our list. To ensure that your paper is linked to the correct gene by AspGD (and other databases), it's always a good idea to include the gene name, systematic name, and species name (e.g. "Aspergillus nidulans" or "A. nidulans") in the abstract. If you think we might have missed your paper, please send us an email and we will be happy to add it.
AspGD is currently soliciting input from the Aspergillus research community regarding the gene nomenclature guidelines and a gene name reservation system similar to the system implemented at the Candida Genome Database.
Please see the AspGD Sequence Documentation web page for information about the genomic sequence.
For help using the GBrowse Genome Browser, please see our GBrowse Help Documentation page.
Sequence issues pertaining to individual genes are described in the Locus History, which may be accessed using the link under "Additional Information" near the bottom of the gene's Locus Summary page.
AspGD maintains a list of publications describing AspGD, written by AspGD staff, that can be used as references to AspGD as a database.
For references to the data contained within AspGD, the original published references should be cited wherever possible. For unpublished information, you should get permission directly from the investigator who submitted the data to AspGD if there is a contact listed for that information. Further instructions on how to cite AspGD and other electronic resources may be found on the How to Cite AspGD page.
AspGD help resources are listed on the Help Resources page. The 'Help' button in the upper right corner of each tool and Locus Summary page is linked directly to help documentation for that particular page.
Getting Started with AspGD provides an introductory overview of AspGD and how to use it.
The Glossary page, provided by the Saccharomyces Genome Database (SGD), lists definitions of genetic, bioinformatic, and other terms used in AspGD and SGD.
AspGD curators may be contacted using our suggestion form. We welcome your comments and questions!
GO is a collaborative project, involving AspGD and other model organism databases, to provide controlled vocabularies that are used to describe the molecular function and cellular location of gene products and the biological process in which they are involved. The three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. The development of the ontologies is ongoing in order to incorporate new information.
The GO Consortium website is the central repository for GO information and documentation, and for the ontologies themselves. SGD's GO Help page provides a brief introduction to GO, and the SGD GO tutorial is a guided tour of GO annotations and of the GO tools that are used at SGD and at AspGD.
Whenever a GO term is displayed on an AspGD Locus Summary page, that term is hyperlinked to a list of all gene products annotated to that term in AspGD. You can search for a particular GO term by typing all or part of the term into the Quick Search box at the top of most AspGD pages. This will return a list of all terms matching the search criterion, along with lists of gene products annotated to each term.
AspGD has two tools for analysis of GO classifications of groups of genes. The GO Slim Mapper tool takes a set of genes specified by the user and maps each to higher-level GO-Slim terms. The GO Term Finder tool takes the user's set of genes of interest and finds GO terms that are shared within the set. Detailed documentation is available on the GO Slim Mapper help page and the GO Term Finder help page, provided by SGD.
In assigning Gene Ontology (GO) terms, our aim is to annotate each function, process, and location of the gene product with the full set of references that establish the classification. This curation is not yet complete. If your paper has not been cited, feel free to send us an email, and we will add the information as quickly as possible.
Both Aspergillus nidulans and Emericella nidulans refer to the same species, at different stages of its life cycle. Aspergillus nidulans is an "imperfect" stage (anamorph) that reproduces asexually through conidia, whereas Emericella nidulans is a sexually reproducing stage (teleomorph) that produces fruiting bodies, cleistothecia, containing asci with ascospores. Currently, the name Aspergillus nidulans is predominantly used to refer to this species.
Unfortunately, we cannot directly help you because AspGD is a scientific database that provides information about the molecular biology and genetics of the fungal genus Aspergillus to researchers. To find out more information about fungal infections, you can go to a medical library at a local university, search the PubMed database for relevant literature, or browse the Aspergillosis information at MEDLINE Plus. We are not medical doctors and we cannot give medical advice. Please speak to a qualified physician about any medical concerns that you might have.
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AspGD Copyright © 2008-2013 The Board of Trustees, Leland Stanford Junior University, and Broad Institute.
Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
To cite AspGD, please use the following reference: Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2013). The Aspergillus Genome Database (AspGD): multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res. 42(Database issue):D705-D710; see How to cite AspGD.