Tools   Select Another Resource Report Type

https://omictools.com/protein-interactions-and-molecular-information-database-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. PRIME is a developed version of Kinase Pathway Database which is an integrated database concerning completed sequenced major eukaryotes, which contains the classification of protein kinases and their functional conservation and orthologous tables among species, protein-protein interaction data, domain information, structural information, and automatic pathway graph image interface. The protein-protein interactions are extracted by natural language processing (NLP) from abstracts using basic word pattern and protein name dictionary GENA: developed by our group. In this system, pathways are easily compared among species using protein interactions data more than 1,510,000 and orthologous tables. Further, using other organisms interaction data, interaction prediction is also possible.

Proper citation: Protein interaction and molecular information database (RRID:SCR_002096) Copy   

•   Source: SciCrunch Registry

http://pathway.gramene.org/gramene/ricecyc.shtml

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 5 of the TIGR-assembly of Oryza sativa japonica cv. Nipponbare genome sequenced by IRGSP.

Proper citation: Rice Metabolic Pathway Database (RRID:SCR_002128) Copy   

•   Source: SciCrunch Registry

http://www.homozygositymapper.org/

A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)

Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy   

•   Source: SciCrunch Registry

http://pstiing.icr.ac.uk/

A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis.

Proper citation: pSTIING (RRID:SCR_002045) Copy   

•   Source: SciCrunch Registry

http://pallab.serc.iisc.ernet.in/gester/

Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed.

Proper citation: WebGeSTer DB (RRID:SCR_002165) Copy   

•   Source: SciCrunch Registry

http://lepr.ofm-research.org/

Database of results of published experimental studies involving liquid-solid phase equilibria relevant to natural magmatic systems.

Proper citation: Library of Experimental Phase Relations (RRID:SCR_002202) Copy   

•   Source: SciCrunch Registry

http://www.ddg-pharmfac.net/antijen/AntiJen/antijenhomepage.htm

Database with quantitative binding data for peptides binding to various cells including MHC Ligand, TCR-MHC complexes, T-cell epitopes, TAP, B-cell, and immunological protein-protein interactions. Information in each entry includes peptide libraries, copy numbers, and diffusion coefficient data.

Proper citation: AntiJen (RRID:SCR_001750) Copy   

•   Source: SciCrunch Registry

http://stke.sciencemag.org/cm/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. This database provides information on the components of cellular signaling pathways and their relations to one another, which are organized into pathways called Connections Maps, which serve as the graphical interface into the database. Access to the database is free. Scientists with expertise in a given field, designated as Pathway Authorities, provide the information. With canonical or general data about cell signaling, as well as specific data about particular signaling processes in specific organisms and cells, there is information for both novices to cell signaling and experts. The Connections Maps are dynamically generated graphical interface to a database of information on the components of cellular signaling pathways and their relations to one another. Information is provided by pathway authorities with expertise in a given field. These Maps provide information on Canonical Pathways -- idealized or generalized pathways that represent common properties of a particular signaling module or pathway. Sponsors: This database is supported by AAAS.

Proper citation: Signal Transduction Knowledge Environment - Database of Cell Signaling (RRID:SCR_001861) Copy   

•   Source: SciCrunch Registry

http://eyelab.biostr.washington.edu/repos/eyelab_repo/

The Image Repository contains a collection of images produced by the research of John Clark's Eye Lab. Experiments include: Irradiated CP49 KO and wildtype, Hypothesis: CP49 KO mice will be more sensitive to X-irradiation than controls Huntington Mice Cataract ID, Hypothesis: Individuals can be identified by the pattern of their cataract. Alpha-Synuclein Mice, Hypothesis: Mice transgenic for the EGFP-tagged, mutant and WT strains of human alpha-synuclein gene, will provide a model for the testing of drugs on aggregation of the protein. alpha B Crystallin/SPARC DKO, Hypothesis: The absence of the chaperone protein, alpha B-Crystallin, causes a greater intensity and earlier onset in the opacifying effects of an absence of the matricellular protein, SPARC. Survey of SPARC KO and WT Survey of SPARC KO and WT Mice The repository is being built through a collaboration between the University of Washington's Department of Biological Structure, led by John Clark, and the Structural Informatics Group, led by Jim Brinkley. As an aim of the Biomedical Information Sciences Technology Initiative (BISTI), members of the Structural Informatics Group have been talking with biomedical researchers to find out their informatics needs. Tools such as this repository are being created in response to those needs. This web tool allows the researchers to add their images to a repository facilitating the organization and management of their data.

Proper citation: The Eye Lab Image Database (RRID:SCR_002038) Copy   

•   Source: SciCrunch Registry

https://www.bgee.org/

Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species. Bgee is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of gene expression.

Proper citation: Bgee: dataBase for Gene Expression Evolution (RRID:SCR_002028) Copy   

•   Source: SciCrunch Registry

https://enigma.lbl.gov/regprecise/

Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RegPrecise (RRID:SCR_002149) Copy   

•   Source: SciCrunch Registry

http://eyegene.ophthy.med.umich.edu/madeline/

Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review.

Proper citation: MADELINE (RRID:SCR_001979) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/Resources/record/nlx_144509-1/f2172664-1499-555d-9e84-3b7768695e4d/search?q=integrated&l=integrated

Virtual database of individual data sources, maintained by SciCrunch participating groups. Database topics are varied, including animals, grants, software, brain gene expression, and clinical trials.

Proper citation: Integrated (RRID:SCR_002187) Copy   

•   Source: SciCrunch Registry

http://giladlab.uchicago.edu/orthoExon/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. It can be used in analysis of multi-species RNA-seq expression data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms.

Proper citation: Primate Orthologous Exon Database (RRID:SCR_002065) Copy   

•   Source: SciCrunch Registry

http://atgc.lbl.gov/atgc/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. ATGC stands for Alignable Tight Genomic Cluster, which is cluster of closely related prokaryotic genomes. ATGC is the principal notion of this web resource. The purpose of this web resource is to prepare ATGC-derived data sets for a variety of research projects in functional and evolutionary genomics. Unique features of ATGC include: * Reliable identification of orthologs (high degree of similarity between the genomes in the set allow an extensive use of synteny in ortholog identification); * Fine granularity of protein classification (in comparisons of more distant genomes, proteins belonging to families of paralogs are often lumped into a singlegroup; under the ATGC approach, comparison of genomic sequences from highly similar genomes allows one to track each set of orthologs separately); * Relative rarity of changes of any kind (in sequence, genome organization and gene content) allows the use of parsimony-related methods of analysis.

Proper citation: Alignable Tight Genomic Cluster (RRID:SCR_001894) Copy   

•   Source: SciCrunch Registry

http://www.arabidopsisreactome.org

Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context.

Proper citation: Arabidopsis Reactome (RRID:SCR_002063) Copy   

•   Source: SciCrunch Registry

http://ibvd.virtualbrain.org/

A database of brain neuroanatomic volumetric observations spanning various species, diagnoses, and structures for both individual and group results. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as metaanalysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparative analyses. Design strategy: The principle organizing data structure is the "publication". Publications report on "groups" of subjects. These groups have "demographic" information as well as "volume" information for the group as a whole. Groups are comprised of "individuals", which also have demographic and volume information for each of the individuals. The finest-grained data structure is the "individual volume record" which contains a volume observation, the units for the observation, and a pointer to the demographic record for individual upon which the observation is derived. A collection of individual volumes can be grouped into a "group volume" observation; the group can be demographically characterized by the distribution of individual demographic observations for the members of the group.

Proper citation: Internet Brain Volume Database (RRID:SCR_002060) Copy   

•   Source: SciCrunch Registry

http://www.earthchem.org/seddb

Geochemical database for marine and terrestrial sediments primarily from the published literature containing a full range of analytical values for sediment samples, primarily from marine sediment cores. It includes major and trace element concentrations, radiogenic and stable isotope ratios, and data for a plethora of materials such as organic and inorganic components, leachates, and size fractions. SedDB also archives a vast array of metadata relating to the individual sample.

Proper citation: SedDB (RRID:SCR_002210) Copy   

•   Source: SciCrunch Registry

http://www.epmba.org/

The Electronic Prenatal Mouse Brain Atlas, EPMBA, at present consists of two sets of annotated images of coronal sections from Gestational Day (GD) 12 heads and GD 16 brains of C57BL/6J mice. Ten micron thick sections were stained with hematoxylin and eosin. Images were prepared at various resolutions for annotations and for high resolution presentation. A subset of sections were annotated and linked to anatomical terms. Additionally, horizontal sections of a GD 12 head were aligned and re-assembled into a 3D volume for digital sectioning in arbitrarily oblique planes. These images were captured using a Nikon E800 stereomicroscope with a 10X objective. The resolution is 1.35 pixels/micrometer. The PC program used to grab the images, Microbrightfield's Neurolucida (version 6), stitched together a mosaic of between 10 and 50 high-res images for each tissue slice, while the user focused the scope for each mosaic tile. Since the nature of optic lenses is to focus on one central point, it was difficult to obtain a uniformly-focused field of vision; as such, small areas of these images are blurred. Images were then transferred to a Macintosh and processed in Adobe Photoshop (version 7). Color levels were adjusted for maximum clarity of the tissue, and areas surrounding the tissue were cleared of artifacts. Each image is approximately 3350 pixels wide by 2650 pixels high. A scale bar with a length of 1350 pixels/mm is visible in the lower right-hand corner of each image. The annotations have been completed for the Atlas of Developing Mouse Brain Gestational (Embryonic) Day 12 (7/5/07) as well as the Atlas of Developing Mouse Brain Embryonic Day 16 (4/26/07). The 3D EPMBA data set has been mounted on a NeuroTerrain Atlas Server (NtAS). (6/27/07).

Proper citation: EPMBA.ORG: Electronic Prenatal Mouse Brain Atlas (RRID:SCR_001882) Copy   

•   Source: SciCrunch Registry

http://www.earthchem.org/petdb

Accepts and provides access to geochemical and petrological data for ocean floor igneous and metamorphic rocks, (whole rock, volcanic, glass, mineral, and melt inclusion analyses), and mantle and lower-crustal xenolith samples. Data are compiled primarily from the published literature. Authors are encouraged to submit their datasets and databases to EarthChem.

Proper citation: PetDB (RRID:SCR_002209) Copy   

•   Source: SciCrunch Registry