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Category:Resource:Blip: Biomedical Logic Programming
Abbrev Blip, blipkit  +
Availability GNU Lesser General Public License +
CurationStatus curated  +
DefiningCitation  +
Definition Biomedical Logical Programming (Blip) is a Biomedical Logical Programming (Blip) is a research-oriented deductive database and prolog application library for handling biological and biomedical data. It includes packages for advanced querying of ontologies and annotations. Blip underpins the Obol tool. Here are some distinguishing characteristics of Blip * Lightweight. Bloat-free: Blip only has as many modules as it needs to do its job. * Fast. * Declarative. Say what you want to do, not how you want to do it * Blip can be Query-oriented: specify your data sources and ask your query * Blip can be Application-oriented: it is designed to be used as an application library used by other bioinformatics tools * Mature and fully functional ontology module for handling both OBO-style ontologies and OWL ontologies. * Modules for handling biological sequences and sequence features. (currently limited functionality, added as needed) * A systems biology module for querying pathway and interaction data. (currently limited functionality, added as needed) * Relational database integration. SQL can be viewed as a highly restricted dialect of Prolog. Although the SWI-Prolog in-memory database is fast and scalable, sometimes it is nice to be able to fetch data from an external database. Blip contains a generic SQL utility module and predicate mappings for the GO database, Ensembl and Chado * Integration with a variety of bioinformatics file formats. SWI-Prolog has a variety of fast libraries for dealing with XML, RDF and tabular data files. Blip provides bridges from bio file formats encoded using these syntaxes into its native models. For other syntaxes, Blip seamlessly integrates other packages such as BioPerl and go-perl. Although these dependencies require extra installation, there is no point reinventing the wheel * Rapid development of web applications. Blip extends SWI-Prolog's excellent http support with a simple and powerful logical-functional-programming style application server, serval. This has been used to prototype a fully-featured next-generation replacement for the GO project amigo browser. * Scalable. Blip is not intended to be a toy system on toy data (although it is happy to be used as a toy if you like!). It is intended to be used as an application component and a tool operating on real-world biological and biomedical data Blip is written in SWI-Prolog, a fast, robust and scalable implementation of ISO Prolog. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible patible, Linux compatible, Unix compatible
ExampleImage Blip.PNG +
Has default formThis property is a special property in this wiki. Resource  +
Has role Software resource +
Id nlx_149193  +
Is part of Resource:Berkeley Bioinformatics Open-Source Projects +
Keywords Biology +, Biomedical +, Ontology +, Annotation +, Software library +, Bioinformatics +, Module +
Label Resource:Blip: Biomedical Logic Programming  +
Listedby Resource:Gene Ontology Tools +
Modification dateThis property is a special property in this wiki. 11 December 2014 16:45:18  +
ModifiedDate 11 December 2014  +
Page has default formThis property is a special property in this wiki. Resource  +
RelatedTo Resource:GO +
SuperCategory Resource  +
Synonym Blip - Biomedical Logic Programming  +, Biomedical Logic Programming  +, Biomedical Logical Programming (Blip)  +
Categories Resource
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*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.