Disease and Drugs
- 1 C. elegans as a model system to study disease and disease genes
- 2 Human disease relevance descriptions
- 3 WormBase contributions to the Disease Ontology
- 4 Acedb model changes for human disease data in WB
- 5 OA and scripts for disease data
- 6 Textpresso-based systems to flag papers
- 7 Gene-disease association file (DAF)
- 8 Data submission to the Alliance
- 9 C. elegans as infection model
C. elegans as a model system to study disease and disease genes
Human disease relevance descriptions
C. elegans has been established as the simplest animal model available for human disease. We have made orthologs of human disease genes, a priority list for curation. In the past, information about the relevance to human disease was to a large extent based on sequence comparison of the related human gene and it's elegans ortholog. This resulted in a scripted description for the elegans gene, that mentioned the human ortholog, the disease caused when the human gene is mutated, and the related OMIM identifiers. We have now begun a more detailed updating of these descriptions, and the writing of new ones, based on the published literature, where elegans is used to model the biology of a disease and/or the orthologous elegans gene function is studied in detail. We have developed a method to identify and flag these papers using a Textpresso (www.textpresso.org) keyword and category based search.
A new database tag 'Human disease gene relevance' was introduced so that we can highlight and make this data available for use by both the elegans as well as the non-elegans biomedical researcher.
This tag will be used to:
--hold OMIM data that is currently in concise descriptions
--highlight how studies in elegans has contributed to understanding of human disease
Human disease relevance descriptions
Human disease relevance descriptions were introduced in late 2011, on the WormBase gene page, to serve both the worm researcher and the biomedical researcher from outside the worm community. This description alerts researchers to the fact that the worm is either an effective model system or is being developed as a model system to study the disease/gene. For under-studyed genes in elegans for which there are only sequence names, human ortholog and disease information provide clues to the function of the gene.
Human disease relevance descriptions are written in most cases, to include:
- Orthology to the human disease gene or family of genes, may include domain information.
- The different types of human diseases known to have mutations in the human gene ortholog. OMIM accession numbers are provided below the description which are links into the OMIM resource.
- Functional similarities or differences between the human/vertebrate and worm gene.
- Data from worm studies that add new knowledge, or validate existing knowledge from studies in other species or experimental systems (eg., cell culture, etc.).
- For understudyed genes in elegans for which there are only sequence names, human ortholog and disease information provide insights into elegans gene function
- Also serves the purpose of making automated descriptions more information-rich and useful to users:
Examples of automated descriptions based on OMIM orthology that existed in WormBase prior to 2012:
1. T27A3.6 is orthologous to the human gene MOLYBDENUM COFACTOR BIOSYSTHESIS PROTEIN E (MOCS2; OMIM:603708), which when mutated leads to disease.
2. Y24D9A.8 is orthologous to the human gene TRANSALDOLASE 1 (TALDO1; OMIM:602063), which when mutated leads to disease.
3. Y110A7A.9 is orthologous to the human gene KIAA1351 PROTEIN (WDR11; OMIM:606417), which when mutated leads to disease.
For WormBase Progress Report (written May/June 2012)
In recent years, C. elegans has been widely used as a system to study human disease gene orthologs and to model human disease and drug-disease interactions. In early 2012, we began writing ‘Human Disease Relevance’ descriptions, as an addition to the gene pages, keeping in mind the non-worm biomedical community. These descriptions combine information obtained from automated ortholog identification methods which are mostly based on sequence, with curated information about disease modeling, from the published worm literature. These descriptions include the following information: (1) Orthology to the human disease gene or family of genes and domain information (2) Diseases associated with mutations in the human gene, with OMIM accessions which are links into the OMIM resource (Online Mendelian Inheritance in Man; http://www.ncbi.nlm.nih.gov/omim) (3) New information or validations that studies in C. elegans have yielded to the study of disease gene/disease. Currently, we have 80 of these descriptions in the database. --End report--
WormBase contributions to the Disease Ontology
Acedb model changes for human disease data in WB
OA and scripts for disease data
Textpresso-based systems to flag papers
Gene-disease association file (DAF)
Data submission to the Alliance
C. elegans as infection model
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