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https://www.noldus.com/ethovision

Video tracking software that tracks and analyzes the behavior, movement, and activity of any animal.

Proper citation: EthoVision XT (RRID:SCR_000441) Copy   

•   Source: SciCrunch Registry

http://dgcst.ceinge.unina.it/

A database of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts. Human and mouse genomic sequences were compared by BLASTZ. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity. The database can be accessed by gene, chromosomal location, graphic browser, DNA features, and coding regions.

Proper citation: Disease Genes Conserved Sequence Tags Database (RRID:SCR_000760) Copy   

•   Source: SciCrunch Registry

http://mitominer.mrc-mbu.cam.ac.uk/

A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java.

Proper citation: MitoMiner (RRID:SCR_001368) Copy   

•   Source: SciCrunch Registry

http://bodymap.genes.nig.ac.jp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008

Proper citation: BodyMap-Xs (RRID:SCR_001147) Copy   

•   Source: SciCrunch Registry

http://mips.helmholtz-muenchen.de/genre/proj/corum

Database of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, but data from high-throughput experiments is excluded.
The majority of protein complexes in CORUM originates from man (65%), followed by mouse (14%) and rat (14%)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CORUM (RRID:SCR_002254) Copy   

•   Source: SciCrunch Registry

http://www.cisred.org/

Database for conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. The database offers information on atomic motifs, motif groups and patterns. In promoter-based cisRED databases, sequence search regions for motif discovery extend from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons. Many transcription factor binding sites are located in such regions. For each target gene's search region, a base set of probabilistic ab initio discovery tools is used, in parallel, to find over-represented atomic motifs. Discovery methods use comparative genomics with over 40 vertebrate input genomes. In ChIP-seq-based cisRED databases, sequence search regions for motif discovery correspond to significant peaks that represent genome-wide sites of protein-DNA binding. Because such peaks occur in a wide range of genic and intergenic locations, ChIP-seq and promoter-based databases are complementary. Currently, motif discovery for ChIP-seq data uses scan-based approaches that make more explicit use of sets of sequences known to be functional transcription factor binding sites, and that consider a wide range of levels of conservation. For the human STAT1 ChIP-seq database search regions in the target species (human) was selected +/- 300 bp around the ChIP-seq peak maximum. Repeats and coding regions were masked. Multiple sequence alignment were used to assemble orthologous input sequences from other species.

Proper citation: cisRED: cis-regulatory element (RRID:SCR_002098) Copy   

•   Source: SciCrunch Registry

http://genome.imim.es/datasets/abs2005/index.html

Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available.

Proper citation: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters (RRID:SCR_002276) Copy   

•   Source: SciCrunch Registry

http://mint.bio.uniroma2.it/domino/

Open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains. The curation effort aims at covering the interactions mediated by the following domains (SH3, SH2, 14-3-3, PDZ, PTB, WW, EVH, VHS, FHA, EH, FF, BRCT, Bromo, Chromo, GYF). The interactions deposited in DOMINO are annotated according to the PSI MI standard and can be easily analyzed in the context of the global protein interaction network as downloaded from major interaction databases like MINT, INTACT, DIP, MIPS/MPACT. It can be searched with a versatile search tool and the interaction networks can be visualized with a convenient graphic display applet that explicitly identifies the domains/sites involved in the interactions.

Proper citation: DOMINO: Domain peptide interactions (RRID:SCR_002392) Copy   

•   Source: SciCrunch Registry

http://www.ariadnegenomics.com/products/databases/resnet/

Databases that represent sets of pre-compiled information on biological relationships and associations, interactions and facts which have been extracted from the biomedical literature using Ariadne's MedScan technology. ResNet databases store information harvested from the entire PubMed in a formal structure that allows searching, retrieval and updating by Pathway Studio user. ResNet is seamlessly installed when Pathway Studio is installed. There are several available ResNet databases: *ResNet Mammalian Database includes data for Human, Rat, and Mouse *ResNet Plant Database has data on Arabidopsis, Rice and several other plants. Features of ResNet: *All extracted relations have linked access to the original article or abstract *Synonyms and homologs are included to maintain gene identity and to obviate redundancy in search results *Users can update ResNet as often as required using the MedScan technology built into all Ariadne products *Updates are made available by Ariadne every quarter To purchase Pathway Studio software with ResNet database, for information, or to schedule a web demonstration, call our sales department at (240) 453-6272, or (866) 340-5040 (toll free)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RESNET (RRID:SCR_002121) Copy   

•   Source: SciCrunch Registry

http://dbtss.hgc.jp/

Database of transcriptional start sites (TSSs) representing exact positions in the genome based on a unique experimentally validated TSS sequencing method, TSS Seq. A major part of human adult and embryonic tissues are covered. DBTSS contains 491 million TSS tag sequences collected from a total of 20 tissues and 7 cell cultures. Also integrated is generated RNA-seq data of subcellular- fractionated RNAs and ChIP Seq data of histone modifications, RNA polymerase II and several transcriptional regulatory factors in cultured cell lines. Also included is external epigenomic data, such as chromatin map of the ENCODE project. They associated those TSS information with public and original SNV data, in order to identify single nucleotide variations (SNVs) in the regulatory regions.

Proper citation: DBTSS: Database of Transcriptional Start Sites (RRID:SCR_002354) Copy   

•   Source: SciCrunch Registry

http://www.germonline.org/

Cross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: GermOnline (RRID:SCR_002807) Copy   

•   Source: SciCrunch Registry

http://karg.cbi.pku.edu.cn

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database of data and knowledge linking genes and chromosome regions to addiction that were extracted from reviewing more than 1,000 peer-reviewed publications from between 1976 and 2006. This list of publications included review papers on addiction selected from results of PUBMED query "(addiction OR drug abuse) AND review" as well as research papers selected from PUBMED query "(addiction OR drug abuse) AND (gene OR microarray OR proteomics OR QTL OR population association OR genetic linkage)". The data spanned multiple technology platforms including classical hypothesis-testing of single genes, identification of significantly differentially expressed genes in microarray experiments, identification of significantly differentially expressed proteins in proteomics assays, identification of addiction-vulnerable chromosome regions in animal QTL studies, genetic linkage studies, population association studies, and OMIM annotations. From each publication they collected the genes, proteins, or chromosome regions linked to addiction, as well as metadata such as species, nature of the addictive substance, studied brain regions, technology platforms, and experimental parameters. In total, they collected 2,343 items of evidence linking 1,500 human genes to addiction. Among them 396 genes were supported by two or more items of evidence. The interface supports browsing of the genes by chromosome or pathways, advanced text search by gene ID, organism, type of addictive substance, technology platform, protein domain, and/or PUBMED ID, and sequence search by BLAST similarity. All data, database schema, and MySQL commands are freely available for download.

Proper citation: Knowledgebase for Addiction Related Genes (RRID:SCR_002687) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/mapview/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.

Proper citation: MapViewer (RRID:SCR_003092) Copy   

•   Source: SciCrunch Registry

https://confluence.crbs.ucsd.edu/display/NIF/DRG

Gene expression data from published journal articles that test hypotheses relevant to neuroscience of addiction and addictive behavior. Data types include effects of particular drug, strain, or knock out on particular gene, in particular anatomical region. Focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data are available for query through NIF interface.Data submissions are welcome.

Proper citation: Drug Related Gene Database (RRID:SCR_003330) Copy   

•   Source: SciCrunch Registry

http://rgd.mcw.edu/rgdCuration/?module=portal&func=show&name=nuro

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools.

Proper citation: Rat Genome Database: Neurological Disease Portal (RRID:SCR_008685) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/searches/MP_form.shtml

Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome.

Proper citation: MPO (RRID:SCR_004855) Copy   

•   Source: SciCrunch Registry

http://bluebrain.epfl.ch/

A Swiss-led project with the aim of reverse engineering the mammalian brain and achieving a complete virtual human brain. The researchers have demonstrated the validity of their method by developing a realistic model of a rat cortical column, consisting of about 10,000 neurons. The eventual goal is to simulate systems of millions and hundreds of millions of neurons. The virtual brain will be an exceptional tool giving neuroscientists a new understanding of the brain and a better understanding of neurological diseases. In five years of work, Henry Markram's team has perfected a facility that can create realistic models of one of the brain's essential building blocks. This process is entirely data driven and essentially automatically executed on the supercomputer. Meanwhile the generated models show a behavior already observed in years of neuroscientific experiments. These models will be basic building blocks for larger scale models leading towards a complete virtual brain.

Proper citation: Blue Brain Project (RRID:SCR_002994) Copy   

•   Source: SciCrunch Registry

http://www.uniprot.org/program/Chordata

Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms.

Proper citation: UniProt Chordata protein annotation program (RRID:SCR_007071) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-8/search?q=*

A data set of connectivity statements from BAMS, CoCoMac, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal Table of Temporal-Lobe.com, and Avian Brain Circuitry Database. The data set lists which brain sites connectivity is to and from, the organism connectivity is mapped in, and journal references.

Proper citation: Integrated Nervous System Connectivity (RRID:SCR_006391) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-7/search?q=*

Virtual database currently indexing interaction between genes and diseases from Online Mendelian Inheritance in Man (OMIM) and Comparative Toxicogenomics Database (CTD).

Proper citation: Integrated Gene-Disease Interaction (RRID:SCR_006173) Copy   

•   Source: SciCrunch Registry