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http://massgenomics.org/

Blog discussing next-generation sequencing and medical genomics in the post-genome era. Most posts are in-depth reviews of recent research publications or editorials.

Proper citation: MassGenomics (RRID:SCR_001018) Copy   

•   Source: SciCrunch Registry

http://www.diacomp.org

Consortium serving the diabetic complications community that sponsors annual meetings in complications-relevant scientific areas, solicits and funds pilot projects in high impact areas of complications research, and provides resources and data including animal models, protocols and methods, validation criteria, reagents and resources, histology, publications and bioinformatics for researchers conducting diabetic complications research.

Proper citation: Diabetic Complications Consortium (RRID:SCR_001415) Copy   

•   Source: SciCrunch Registry

http://cellularscale.blogspot.com/

Blog focusing on cellular-level neuroscience for everyone. While a higher level of neuroscience, such as behavioral studies and human fMRI scans level of neuroscience is interesting to everyone, some people might want to focus a little closer in. That is what The Cellular Scale is for.

Proper citation: Cellular Scale (RRID:SCR_001379) Copy   

•   Source: SciCrunch Registry

http://pc1664.pharmazie.uni-marburg.de/affinity/

Database of affinity data for protein-ligand complexes of the Protein Data Bank (PDB) providing direct and free access to the experimental affinity of a given complex structure. Affinity data are exclusively obtained from the scientific literature. As of Thursday, May 01st, 2014, AffinDB contains 748 affinity values covering 474 different PDB complexes. More than one affinity value may be associated with a single PDB complex, which is most frequently due to multiple references reporting affinity data for the same complex. AffinDB provides access to data in three different forms:
# Summary information for PDB entry
# Affinity information window
# Tabular reports

Proper citation: AffinDB (RRID:SCR_001690) Copy   

•   Source: SciCrunch Registry

https://chordate.bpni.bio.keio.ac.jp/chordate/faba/1.4/top.html

Image resource including ascidian's three-dimensional (3D) and cross-sectional images through the developmental time course. These images were reconstructed from more than 3,000 high-resolution real images collected by confocal laser scanning microscopy (CLSM) at newly defined 26 distinct developmental stages (stages 1-26) from fertilized egg to hatching larva, which were grouped into six periods named the zygote, cleavage, gastrula, neurula, tailbud, and larva periods. The data set will be helpful in standardizing developmental stages for morphology comparison as well as for providing guidelines for several functional studies of a body plan in chordate.

Proper citation: Four-dimensional Ascidian Body Atlas (RRID:SCR_001691) Copy   

•   Source: SciCrunch Registry

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17493288

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. LinkHub is a software system using Semantic Web RDF that manages the graph of identifier relationships and allows exploration with a variety of interfaces. It leverages Semantic Web standards-based integrated data to provide novel information retrieval to identifier-related documents through relational graph queries, simplifies and manages connections to major hubs such as UniProt, and provides useful interactive and query interfaces for exploring the integrated data. For efficiency, it is also provided with relational-database access and translation between the relational and RDF versions. LinkHub is practically useful in creating small, local hubs on common topics and then connecting these to major portals in a federated architecture; LinkHub was used to establish such a relationship between UniProt and the North East Structural Genomics Consortium. LinkHub also facilitates queries and access to information and documents related to identifiers spread across multiple databases, acting as connecting glue between different identifier spaces. LinkHub is available at hub.gersteinlab.org and hub.nesg.org with supplement, database models and full-source code. Sponsors: Funding for this work comes from NIH/NIGMS grant P50 GM62413-01, NIH grant K25 HG02378, and NSF grant DBI-0135442.

Proper citation: LinkHub: A Semantic Web System that facilitates cross-database queries and information retrieval in proteomics (RRID:SCR_001844) Copy   

•   Source: SciCrunch Registry

http://mech.ctb.pku.edu.cn/protisa/

Database of confirmed translation initiation sites (TISs) for prokaryotic genomes. The confirmed data has supporting evidence from different sources, including experiments records in the public protein database Swiss-Prot, literature, conserved domain search and sequence alignment among orthologous genes. Combing with predictions from the-state-of-the-art TIS predictor MED-Start/MED-StartPlus (in release 1.0 & 1.2) and TriTISA (since release 1.4) and annotations on potential regulatory signals, the database can serve as a refined annotation resource for the public database RefSeq.

Proper citation: ProTISA (RRID:SCR_002138) Copy   

•   Source: SciCrunch Registry

http://django.nubic.northwestern.edu/fundo/

Tool that takes a list of genes and finds relevant diseases based on statistical analysis of the Disease Ontology annotation database. It accepts Entrez gene ids or gene symbols, separated by tabs, newlines, or commas. This list of genes can be obtained by microarray, proteomics, sequencing or other high-throughput screening methods.

Proper citation: FunDO (RRID:SCR_001725) Copy   

•   Source: SciCrunch Registry

https://epd.expasy.org/epd/

Collection of eukaryotic promoters derived from published articles. Annotated non-redundant collection of eukaryotic POL II promoters, for which transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.

Proper citation: Eukaryotic Promoter Database (RRID:SCR_002132) Copy   

•   Source: SciCrunch Registry

http://caps.ncbs.res.in/stifdb2/

Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method.

Proper citation: STIFDB (RRID:SCR_002131) Copy   

•   Source: SciCrunch Registry

http://www.cisreg.ca/tfe

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.The TFe provides details of transcription factor binding sites in close collaboration with Pazar, a public database of transcription factor and regulatory sequence information. The long-term goal of TFe is to create an online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes, combining a mixture of both expert-curated and automatically-populated content to provide users with a wide set of information relevant to a transcription factor protein of their interest.

Proper citation: Transcription Factor encyclopedia (RRID:SCR_002130) Copy   

•   Source: SciCrunch Registry

http://megasun.bch.umontreal.ca/ogmpproj.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. It investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP.

Proper citation: Organelle Genomics (RRID:SCR_002137) Copy   

•   Source: SciCrunch Registry

http://wikipathways.org/

Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community.

Proper citation: WikiPathways (RRID:SCR_002134) Copy   

•   Source: SciCrunch Registry

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