Formalization of biological experiments
From IT SPb Academy
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Minimum Information for Biological and Biomedical Investigations MIBBI
Existing knowledge bases projects
Existing Databases
- UniProt - has some API but it’s very havvy.
- Go - Gene Ontology http://www.geneontology.org/
- http://www.geneontology.org/GO.database.shtml#mirrors has SQL acces
- http://wiki.geneontology.org/index.php/Example_Queries
- http://www.ensembl.org/info/data/mysql.html
Biological ontologies
- EFO
- OBI - The Ontology for Biomedical Investigations main page owl
- NCI http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
- MGED The primary purpose of the MGED Ontology is to provide standard terms for the annotation of microarray experiments owl
- Fuge
- The Open Biological and Biomedical Ontologies
- Bio-Ontologies: A List of links
Semantic Network
Курс Конева “Онтология и представление знаний“ http://logic.pdmi.ras.ru/csclub/courses/ontology
OWL Semantic Web for the Working Ontologist: Effective Modeling in RDFS and OWL
Misha Kapushesky
Форма для отправки экспериментов в MAGE-TAB link.
Пример сложного эксперимента img.
Самый большой эксперимент link.
MAGE-TAB
Full MAGE ML specification
Programmatic Access to ArrayExpress
Other
R bioinformatics; Gene Networks; MAGE TAB editor tutorial
GGA Software Services - Фирма с отделением в Санкт-Петербурге, которая знанимается разработкой биологического ПО.
