BIO 3012 - Research Methods

National Center for Biotechnology Information, U.S. National Library of Medicine

"canSAR is an integrated knowledge-base that brings together multidisciplinary data across biology, chemistry, pharmacology, structural biology, cellular networks and clinical annotations, and applies machine learning approaches to provide drug-discovery useful predictions". --website

"The use of ConsensusPathDB is free for academic users. ... ConsensusPathDB is being developed by the Bioinformatics group of the Vertebrate Genomics Department at the Max-Planck-Institute for Molecular Genetics in Berlin, Germany."--website

The Enzyme Portal is for those interested in the biology of enzymes and proteins with enzymatic activity.

Pathogen Portal is a repository linking to the Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID) and maintained by The Virginia Bioinformatics Institute.

"Pathway Commons is a network biology resource and acts as a convenient point of access to biological pathway information collected from public pathway databases, which you can search, visualize and download. All data is freely available, under the license terms of each contributing database."-- "Pathway Commons is built and maintained by Memorial Sloan-Kettering Cancer Center and the University of Toronto."-- website

"InterMine is an open source data warehouse built specifically for the integration and analysis of complex biological data. Developed by the Micklem lab at the University of Cambridge, InterMine enables the creation of biological databases accessed by sophisticated web query tools."--website

The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI.

"GeneCards is a searchable, integrated database of human genes that provides comprehensive, updated, and user-friendly information on all known and predicted human genes.GeneCards extracts and integrates gene-related data, including genomic, transcriptomic, proteomic, genetic, clinical, and functional information. This is automatically mined from >100 carefully selected web sources... Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science. Free for academic non-profit institutions."--website

"This site contains the reference sequence and working draft assemblies for a large collection of genomes.

"The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online. ... Ensembl is a joint project between EMBL - EBI and the Wellcome Trust Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes."--website

The Ensembl genome annotation system, developed jointly by the EBI and the Wellcome Trust Sanger Institut

"A repository for high-quality gene models produced by the manual annotation of vertebrate genomes.... Wellcombe Trust, Sanger Institute"--website

PATRIC is a NIH-NIAID -funded project of Virginia Tech’s Cyberinfrastructure Division."

"FlyBase is supported by a grant from the National Human Genome Research Institute at the U.S. National Institutes of Health"--website
Support is also provided by the British Medical Research Council, the Indiana Genomics Initiative, and the National Science Foundation
through XSEDE resources provided by Indiana University

A resource of te U.S. Department of Energy Joint Genome Institute (DOE JGI), provides databases of many eukaryote and microbial genomes.

"RegulonDB is the primary database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions."-- website

The SGD database is "the community resource for the budding yeast Saccharomyces cerevisiae."--website

"Xenbase's mission is to provide the international research community with a comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research." -- website

"The SEED is a framework to support comparative analysis and annotation of genomes."--website

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.

"BioCyc is a collection of 3563 Pathway/Genome Databases (PGDBs), with tools for understanding their data."--website.

Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data.

GreenPhylDB is a web resource designed for comparative and functional genomics in plants. The database contains a catalogue of gene families based on gene predictions of genomes, covering a broad taxonomy of green plants.

"The EnsEMBL database was used to decide on a set of 1-to-1 orthologous markers from those mammalian genomes available. Exons of reasonable length for further amplification from genomic DNA and sequencing in additional species were then selected. For phylogenomic purposes, CoDing Sequences (CDSs) were also collected. The phylogenetic utility and the evolutionary characteristics of these candidate markers were then evaluated using a homemade bioinformatics pipeline. The resulting OrthoMaM database can be interrogated through this website.

NetPath is a manually curated resource of signal transduction pathways in humans. It is a collaborative effort between the PandeyLab at Johns Hopkins University and the Institute of Bioinformatics.

"REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases."--website

WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways.

"BioCyc is a collection of 3563 Pathway/Genome Databases (PGDBs), with tools for understanding their data."--website.

"MetaboLights is a database for Metabolomics experiments and derived information."--website

"The database is a repository for functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are either submitted directly to ArrayExpress and curated by a team of specialist biological curators, or are imported systematically from the NCBI Gene Expression Omnibus database on a weekly basis."--website. MBL-EBI, Wellcome Trust Genome Campus

"GEO is a public functional genomics data repository supporting MIAME-compliant data submissions."--website.

"maxd is a data warehouse and visualisation environment for genomic expression data. It is being developed in the University of Manchester by the Microarray Bioinformatics Group."--website

Bgee is a database to retrieve and compare gene expression patterns between animal species."--website

"This database will enable the reliable identification of an individual IRG or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It will also assist in identifying regulatory elements, chromosomal location and tissue expression of IRGs in human and mouse. This upgraded version, Interferome v2.0 has quantitative data, more detailed annotation and search capabilities and can be queried for one gene or thousands as in a gene list from a microarray experiment." -- website

LncRNAdb is a database providing comprehensive annotations of eukaryotic long non-coding RNAs (lncRNAs). It is now currently maintained by the Genome Informatics Group

"The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR)"--website

"piRNABank is a web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals namely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila. ... Copyright of Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore, India"

"The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs)"--website. European Molecular Biology Laboratory

"The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.... Center for Microbial Ecology, Michigan State University"--website

"A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data. ... SILVA uses a dual licensing model. In short, browsing and deploying the SILVA database."-- website

This site is maintained by Wayne Decatur of the Fournier Lab in Department of Biochemistry and Molecular Biology.

RPDB (Signal Recognition Particle Database) provides aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP. Christian Zwieb, Department of Biochemistry, University of Texas Health Science Center

The tmRDB is a tool in the study of the structures and functions of the tmRNA.

"CATH is a classification of protein structures downloaded from the Protein Data Bank. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor."--website by I. Sillitoe, T. Lewis, D. Lee, J. Lees, C. Orengo is licensed under a Creative Commons Attribution 4.0 International License.
Based on work at http://cath.biochem.ucl.ac.uk.

EMBL-EBI, Wellcome Trust Genome Campus, EBI is an outstation of the European Molecular Biology Laboratory

"PMP gives access to various models computed by comparative modeling methods provided by different partner sites, and provides access to various interactive services for model building, and quality assessment." -- website.

Research Collaboratory for Structural Bioinformatics (RCSB). An Information Portal to Biological Macromolecular Structures.

"SCOP2 is a successor of Structural classification of proteins (SCOP). Similarly to SCOP, the main focus of SCOP2 is on proteins that are structurally characterized and deposited in the PDB. Proteins are organized according to their structural and evolutionary relationships, but, in contrast to SCOP, instead of a simple tree-like hierarchy these relationships form a complex network of nodes. Each node represents a relationship of a particular type and is exemplified by a region of protein structure and sequence ... This is a beta release and contains a fraction of protein structure data."--website

SCOP was created in 1994 in the Centre for Protein Engineering and the Laboratory of Molecular Biology.

SWISS-MODEL is a fully automated protein structure homology-modelling server.

"The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (thebiogrid.org)." --website.

© CCSB Center for Cancer Systems Biology

"The Cell Collective technology allows laboratory scientists working in different areas of the cell to collectively integrate their knowledge and create large-scale virtual cells in a non-technical fashion. ... The Cell Collective is free for academic use."--website

"The Catalog of Inferred Sequence Binding Proteins of RNA (CISBP-RNA) is a library of RNA binding protein (RBP) motifs and specificities."--website

"The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions."--website.

"A reference index for protein interaction data."-- website

"RBPDB is a collection of RNA-binding proteins linked to a curated database of published observations of RNA binding."--website

"STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations"--website

Copyright UCLA. The DIPTM database catalogs experimentally determined interactions between proteins.

nterPro is a resource that provides functional analysis of protein sequences

OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.

A Munich Information Center for Protein Sequences/German Research Center for Environmental Health resource.

Pfam version 27.0 was produced at the European Bioinformatics Institute using a sequence database called Pfamseq, which is based on UniProt release 2012_06.

PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family. A University of Manchester resource.

PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains.

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data.

"LimbformDB is an experiment-phenotype database of limb regeneration data published in the literature. Currently, it contains more than 800 different experiments." -- website

"PhenomicDB is a multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms.
The inclusion of gene indices (NCBI Gene) and orthologues (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously.
PhenomicDB contains data from publicly available primary databases: FlyBase, Flyrnai.org, WormBase, Phenobank, CYGD, MatDB, OMIM, MGI, ZFIN, SGD, DictyBase, NCBI Gene, and HomoloGene."--website

"PHI-base is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. PHI-base is therfore an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, PHI-base also includes antifungal compounds and their target genes."--website

"PhytoPath is a new bioinformatics resource that integrates genome-scale data from important plant pathogen species with literature-curated information about the phenotypes of host infection. Using the Ensembl Genomes browser, it provides access to complete genome assembly and gene models of priority crop and model-fungal, oomycete and bacterial phytopathogens. PhytoPath also links genes to disease progression using data from the curated PHI-base resource"--website

"PlanformDB is an experiment-phenotype database of planarian regeneration data published in the literature. Currently, it contains more than 1,000 different experiments."--website

"The Fungal Secretome and Subcellular Proteome, i. e. protein subcellular location, KnowledgeBase (FunSecKB2) was created by Dr. Xiangjia (Jack) Min and John Meinken at Youngstown State University (YSU). It is an expanded version of a previous website built by Gengkon Lum. Dr. Min collected the data and designed the prediction algorithms. John Meinken implemented the database and built the website. Jessica Orr and Stephanie Frazier, undergraduate students, curated secreted proteins from recent literature. The work was supported by a grant from the YSU University Research Council and by a graduate assistantship for John Meinken from the YSU Center for Applied Chemical Biology. This server is supported by YSU."--website

Gelmap is a universal tool for spot visualization on a gel image. University of Hanover Proteomics Department

"MetazSecKB is a knowledgebase for human/animal secretomes as well as human/animal proteins located in other subcellular locations. "--website

MitoMiner is hosted and maintained by the Bioinformatics group at the MRC Mitochondrial Biology Unit. It is built using InterMine, a general purpose open-source data warehouse system. MitoMiner is hosted and maintained by the Bioinformatics group at the MRC Mitochondrial Biology Unit. It is built using InterMine, a general purpose open-source data warehouse system.

A Youngstown State University resource

"The Plant Secretome KnowledgeBase (PlantSecKB) was designed by Dr. Xiangjia (Jack) Min, Gengkon Lum and John Meinken at Youngstown State University (YSU). Gengkon and John, MS graduate students, primarily implemeted the database. Jessica Orr and Stephanie Frazier, undergraduates, curated secreted proteins from recent literature. The work was supported by a grant from the Ohio Plant Biotechnoloy Consortium and a grant from the University Research Council, YSU. This server is supported by YSU."--website

"Plasma Proteome Database (PPD) was developed as a part of Human Proteome Organization's (HUPO) initial effort to characterize human plasma proteome. This is one of the largest resources on proteins reported in plasma and serum. PPD hosts qualitative and quantitative information on proteins (including those from MRM-based assays) reported in plasma and serum and hence serves as reference platform for biomarker discovery. In addition, proteins reported in extracellular vesicle isolated from plasma are also available."--website

"The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence."--website. EMBL-EBI, Wellcome Trust Genome Campus. EBI is an outstation of the European Molecular Biology Laboratory

"UniGene computationally identifies transcripts from the same locus; analyzes expression by tissue, age, and health status; and reports related proteins (protEST) and clone resources. ... National Center for Biotechnology Information, U.S. National Library of Medicine"--website

"The Allen Mouse and Human Brain Atlases are projects within the Allen Institute for Brain Science which seek to combine genomics with neuroanatomy by creating gene expression maps for the mouse and human brain.."--Wikipedia 10/08/2014

"The Antibody Registry was created to give researchers a way to universally identify antibodies used in in the course of their research. The Antibody Registry assigns unique and persistent identifiers to each antibody so that they can be referenced within publications. Unlike antibody names or catalog numbers, these identifiers only point to a single antibody, so that the actual antibody used in your research research can be identified by humans and search engines.."--website

"The Barcode of Life Data Systems (BOLD) is an informatics workbench aiding the acquisition, storage, analysis, and publication of DNA barcode records. By assembling molecular, morphological, and distributional data, it bridges a traditional bioinformatics chasm. BOLD is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases."--website

From the website description: "The Core Science Analytics, Synthesis, and Libraries (CSAS&L) program of the U.S. Geological Survey (USGS) is developing Biodiversity Information Serving Our Nation (BISON), an integrated and permanent resource for biological occurrence data from the United States."

"BioModels Database is a repository of computational models of biological processes. Models described from literature are manually curated and enriched with cross-references. All models are provided in the Public Domain. ... BioModels Database is developed by the BioModels.net team (part of the PST at EMBL-EBI, UK), the Le Novère lab (Babraham Institute, UK) and the SBML Team (Caltech, USA). "--website

"The bioMovies project is supported by: a Higher Education Academic Challenge Grant from the United States Department of Agriculture and the College of Agriculture and Life Sciences at NC State University. ... iteractive digital video for academic enviroments."--website

"CellML is an international collaborative initiative built around open source science and software. The cellml.org website is a community hub for all things CellML. This section contains information about projects, research groups and events within and related to the CellML community."--website

"The NCBI Clone DB replaces and expands upon the former NCBI Clone Registry, which was established during the era of the human and mouse genome projects to represent a broader range of eukaryotic organisms and clone types."--website

"CTD promotes understanding about the effects of environmental chemicals on human health by integrating data from curated scientific literature to describe chemical interactions with genes and proteins, and associations between diseases and chemicals, and diseases and genes/proteins."--website

"Drug2Gene reports relations between genes/proteins and drugs/compounds including bioactivity data where available. The data has been collected from 19 public databases and integrated to provide a 'one-stop shop' for identifying tool compounds for genes or finding all known targets of a drug. ... Copyright © Metalife AG."--website

"Dryad is a nonprofit repository for data underlying the international scientific and medical literature. ... Dryad is a nonprofit organization that provides long-term access to its contents at no cost to researchers, educators or students, irrespective of nationality or institutional affiliation. Dryad is able to provide free access to data due to financial support from members and data submitters. Dryad’s DPCs are designed to sustain its core functions by recovering the basic costs of curating and preserving data. New innovations are enabled by research and development grants and by support from donors."--website

"ExoCarta, an exosome database, provides with the contents that were identified in exosomes in multiple organisms."--website, . Dr. Suresh Mathivanan, Department of Biochemistry
La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria

"EzBioCloud is a portal and cloud computing service specially designed for researchers in the fields of biology, biotechnology and medical science."--website

"an online resource documenting frequencies of pathogenic genetic variations leading to inherited disorders in various populations worldwide. The initial data came from previously published reports as well as from unpublished information contributed from individual researchers prior of publication. ... Data content is freely available to the public and there are no registration requirements for data querying."--website

"Minimotif Miner (MnM) analyzes protein queries for the presence of short contiguous peptide motifs that have a known function in at least one other protein (Minimotifs), Minimotif functions include posttranslational modification of the minimotifs (PTM), binding to a target protein or molecule, and protein trafficking. One major limitation in MnM and other minimotif prediction approaches is that "false positive" minimotifs result from the relatively low sequence complexity of the sequence definition. MnM 3.0 uses a rich semantic model and trained algorithm to reduce false positive predictions. When tested on a large test dataset 39% of validated minimotifs were recovered with all false positives eliminated. This is set as the default filter on MnM 3.0. We suggest that the known biology of the protein query and be used in selecting minimotifs for experimental study."--website

"OpenAlex is a fully open catalog of the global research system. It's named after the ancient Library of Alexandria" -- docs.openalex.org

"Our goal for EcoliWiki is to generate community-based pages about everything related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements." -website

"RTPrimerDB is a public database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisation, and to introduce a certain level of uniformity and standardisation among different laboratories."--website. Ghent University

"SABIO-RK is a curated database containing structured information about biochemical reactions and their corresponding kinetics. It describes participants and modifiers of the reactions, as well as measured kinetic data (including kinetic rate equations) embedded in their experimental and environmental context."--website

"Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment. ... Department of Ecology and Evolution, Biophore, Lausanne University, CH-1015 Lausanne, Switzerland"--website

"This website has been created to provide clinicans and scientists access to a central genetic database for the local population. The existence of population and country-specific databases is very important and valuable for the study of population history, genetic-testing, as well as disease association studies. The availability of allele and genotype frequencies for specific ethnic groups in our population would be useful for the selection of informative genetic markers in association studies involving complex traits or phenotypes. Thus, these led to the creation of this database which contains the allele and genotype frequencies. "--website

"TreeFam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes. ... EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire"--website