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http://empai.iab.keio.ac.jp/

emPAI (exponentially modified protein abundance index), developed by Ishihama et al., is a measure to describe the protein composition in sample solutions. When the total protein amount in the sample is available, emPAI can be converted to the absolute amount of each protein in the sample. emPAI is derived from PAI, which is defined as the number of the observed peptides divided by the number of the observable peptides per protein. We recently found that log (PAI) had linear relationship to the protein amounts, and that emPAI, 10^(PAI)-1, was proportional to the protein amounts for whole cell lysate digested by trypsin. The accuracy of this method was within factor 5, similar or better than determination of abundance by protein staining

Proper citation: Exponentially Modified Protein Abundance Index (RRID:SCR_008616) Copy   

•   Source: SciCrunch Registry

http://openlibrary.org/

Open Library is a project of the non-profit Internet Archive, and is funded in part by a grant from the California State Library. They have a small team of fantastic programmers who have accomplished a lot, but we can''t do it alone! This is an Open project - the software is open, the data is open, the documentation is open, and the site is open. To build it, they need hundreds of millions of book records, a brand new database infrastructure for handling huge amounts of dynamic information, a wiki interface, multi-language support, and people who are willing to contribute their time, effort, and book data. To date, they have gathered about 30 million records (20 million are available through the site now), and more are on the way. They have built the database infrastructure and the wiki interface, and you can search millions of book records, narrow results by facet, and search across the full text of 1 million scanned books. Sponsors: Open Library is funded by a grant from the California State Library.

Proper citation: Open Library (RRID:SCR_008295) 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

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.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

https://interferome.org/interferome/search/showSearch.jspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2022. InterPare is a database server for protein interaction interface information. It contains large-scale interface data of proteins whose 3D-structures are known. Protein interface information is derived from three different methods. InterPare introduces a large-scale protein domain interaction interface database called InterPare. InterPare uses three methods: 1) the Euclidean distance method for checking the distance among subunits in multidomain proteins, 2) Accessible Surface Area (ASA) for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, 3) the Voronoi diagram, a computational geometry method, that uses a mathematical definition of interface regions. InterPare includes tools with different display modes for viewing protein interior, surface, and interaction interfaces.

Proper citation: The Protein Interfaceome Database (RRID:SCR_002126) Copy   

•   Source: SciCrunch Registry

http://neuronbank.org/wiki

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. Platform for Neuroscientists to describe neurons and neural circuitry. Registered users may edit. The ultimate goal is advance the field of Neuromics by creating an encyclopedia of neurons and neural circuitry. NOTE: The database is no longer being maintained due to lack of funding.

Proper citation: NeuronBank (RRID:SCR_002004) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/LSPD/

LSPD provides liver specific gene. It lists ~300 promoter regions responsible for liver specific transcriptions, collect ~400 experimentally verified regulatory regions and elements, provide information on transcription regulation of liver genes, compare transcription regulation of functionally or evolutionarily related genes, and retrieve sequences of the promoter region. Its regulatory elements provides information on transcription regulatory elements, reports the methods for verification of the elements, records binding affinity and regulatory function, and summarizes the site distribution and sequence consensus.

Proper citation: LSPD (RRID:SCR_002125) Copy   

•   Source: SciCrunch Registry

http://tpdb.medchem.ku.edu:8080/protein_database/index.jsp

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 29,2022. This database is an attempt to catalog in a convenient, searchable fashion the publicly available information about the identities of mammalian proteins that become covalently adducted by chemically-reactive metabolites of xenobiotic agents. At present all entries pertain to well-identified proteins that become adducted following defined exposures to known chemical agents in vivo or in cell culture experiments. Results from studies using enzymatic or chemical model systems have not been included but may be in the future. The search functions are relatively simple and intuitive, so most users can go straight to the Search page and begin searching. Additional explanations, examples and information about possible future expansions may be found.

Proper citation: Target Protein Database (RRID:SCR_002124) Copy   

•   Source: SciCrunch Registry