Ariadne ResNet Databases

Category Cross-Omics>Pathway Knowledge Bases/Databases/Tools

Abstract The Ariadne ResNet Databases are a group of pathway analysis databases that represent different sets of pre-compiled information on biological relationships and associations, interactions and facts which have been extracted from the biomedical literature using MedScan (see G6G Abstract Number 20090). There are several available ResNet databases -

Features of ResNet include - 1) All extracted relations have linked access to the original article or abstract; 2) Synonyms and homologs are included to maintain gene identity and to obviate redundancy in search results; 3) Users can update ResNet as often as required using the MedScan technology built into all Ariadne products; 4) Updates are made available by Ariadne every quarter.

ResNet Mammalian Database -

ResNet Mammalian includes pathways and molecular interactions uniquely representing the entire PubMed (14,000,000 abstracts) and 47 full text journals. It contains information and knowledge on over 1.25 million relations for human, rat and mouse, linked to their original literature sources. ResNet Mammalian Database features include -

Over 1.25 million relations for - 1) 106,749 proteins; 2) 47,852 small molecules; 3) 1094 cell processes; 4) 2,301 diseases.

Pathways - 1) 192 manually curated signaling pathways (canonical pathways); 2) 555 Signaling Line Pathways automatically generated as the most likely regulatory path from receptor to transcription factor.

Ontologies - 1) Gene Ontology (GO); 2) Ariadne protein function ontology.

Annotations - 1) Entrez Gene annotations for proteins; 2) PubChem annotations for small molecules; 3) MedScan dictionary annotations for cell processes and diseases.

ResNet Plant Database -

ResNet Plant is a pathway and molecular interaction database for plant researchers, to be used with Pathway Studio pathway analysis software. ResNet Plant Database features include -

7 plant organisms - 1) Arabidopsis, 2) Rice, 3) Barley, 4) Corn, 5) Tomato, 6) Potato, and 7) Tobacco.

Over 70,000 molecular regulatory relations and physical interactions.

382,000-sentence co-occurrence facts for plant proteins, extracted from 72,000 plant-specific abstracts and four plant full-text journals.

Additional features include -

Protein–protein relations - binding, expression regulation, promoter binding, protein modification, etc.

1) Effect of environmental conditions on proteins and metabolites; 2) Regulation by plant hormones.

ResNet Plant allows the investigation of interplay among individual pathways, easy custom pathways building and flexible database navigation - 1) All extracted relations are linked to the original PubMed abstracts; 2) Synonyms and homologs are included to maintain gene identity and to reduce redundancy; 3) Extensive aliasing ensures all relevant information is extracted; 4) Updated information can be added to ResNet Plant as often as every day using MedScan Technology; 4) Quarterly incremental updates are provided by Ariadne. Updates will Not interfere with additions you have made to the database.

ResNet Targeted Databases -

Ariadne has built the following "Targeted Databases" data sets and makes these available on an "as is" basis as seed data sets for interested researchers. ResNet Targeted Databases containing pathways and functional relations are available for three (3) model organisms - Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster. (Note: The previously available Arabidopsis thaliana model data set is now incorporated and forms part of the ResNet Plant Database release.)

All databases contain protein annotations from EntrezGene and can be used for the analysis of gene expression data. The orthologous interactions can be exchanged among different databases to enrich their content.

Additional molecular interaction databases are also available on an "as is" basis -

1) Bos taurus (cow); 2) Canis familiaris (dog); 3) Gallus gallus (chicken); 4) Xenopus laevis (African clawed frog); 5) Danio rerio (zebrafish).

These databases were constructed by importing orthologous protein- protein interactions from the ResNet Mammalian Database. A molecular interaction database for Apis mellifera (bee) was constructed using orthologous interactions from the Drosophila database.

Protein Annotation in ResNet -

ResNet protein annotation is created by using only publicly available data sources. These resources are compiled into a single map file in RNEF XML format that is then imported into ResNet using the Pathway Studio importer.

System Requirements

See requirements for Ariadne Pathway Studio


Manufacturer Web Site Ariadne Genomics, Inc.

Price Contact manufacturer.

G6G Abstract Number 20021

G6G Manufacturer Number 100335