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Found 46 result(s)

Xanthobase

Xanthomonas oryzae pv. oryzae genome database

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<<<!!!<<< The repository is no longer available. No known URL could be resolved successfully. >>>!!!>>>

caNanoLab

cancer Nanotechnology Laboratory

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caNanoLab is a data sharing portal designed to facilitate information sharing in the biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. caNanoLab provides support for the annotation of nanomaterials with characterizations resulting from physico-chemical and in vitro assays and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion.

Organelle Genome Megasequencing Program

OGMP

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The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.

Metlin

The original and most comprehensive MS/MS metabolite database

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METLIN represents the largest MS/MS collection of data with the database generated at multiple collision energies and in positive and negative ionization modes. The data is generated on multiple instrument types including SCIEX, Agilent, Bruker and Waters QTOF mass spectrometers.

IMEx

The International Molecular Exchange Consortium

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The IMEx consortium is an international collaboration between a group of major public interaction data providers who have agreed to share curation effort and develop and work to a single set of curation rules when capturing data from both directly deposited interaction data or from publications in peer-reviewed journals, capture full details of an interaction in a “deep” curation model, perform a complete curation of all protein-protein interactions experimentally demonstrated within a publication, make these interaction available in a single search interface on a common website, provide the data in standards compliant download formats, make all IMEx records freely accessible under the Creative Commons Attribution License

ENCODE

Encyclopedia of DNA Elements

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The ENCODE Encyclopedia organizes the most salient analysis products into annotations, and provides tools to search and visualize them. The Encyclopedia has two levels of annotations: Integrative-level annotations integrate multiple types of experimental data and ground level annotations. Ground-level annotations are derived directly from the experimental data, typically produced by uniform processing pipelines.

RDP

Ribosomal Database Project

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<<<!!!<<< The RDP website is no longer available. A stand-alone version of the RDP Classifier is available on Sorceforge https://sourceforge.net/projects/rdp-classifier/. Instructions for installing a command-line version of RDP Tools can be found at Dr. J.Quensen's Website https://john-quensen.com/tutorials/tutorial-1/ and https://jfq3.gitbook.io/rdptools-docker/rdptools-docker/readme. >>>!!!>>>

NCBI Datasets

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NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

heidICON

Die Heidelberger Bilddatenbank

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heidICON is provided by Heidelberg University Library and is the "Virtual Slide Collection" in progress of organization of Heidelberg University. In addition to record graphic material on current interest for research and teaching, the University departments and institutes can digitize and transfer their already existing slide collections.

ChIP-Seq Transcription Factor Data

ChIP-Seq

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We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in interferon-gamma (IFN-gamma)-stimulated and unstimulated human HeLa S3 cells, and compared the method's performance to ChIP-PCR and to ChIP-chip for four chromosomes.For both Chromatin- immunoprecipation Transcription Factors and Histone modifications. Sequence files and the associated probability files are also provided.

TOXNET

Toxicology Data Network

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<<<!!!<<<The repository is no longer available <<<!!!<<< TOXNET has moved. Most content will continue to be collected and reviewed; selected information is accessible through PubChem, PubMed, and Bookshelf. If you have questions, please contact NLM Customer Support at https://support.nlm.nih.gov/ >>>!!!>>>

IMGT/LIGM-DBI

International ImMunoGeneTics information system / Laboratoire d'ImmunoGénétique Moléculaire-Database

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IMGT/LIGM-DB is a comprehensive database of Immunoglobulins (IG) and T cell Receptors (TR) from human and other vertebrates, with translation for fully annotated sequences.

Morph·D·Base

MorphDBase

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Morph·D·Base has been developed to serve scientific research and education. It provides a platform for storing the detailed documentation of all material, methods, procedures, and concepts applied, together with the specific parameters, values, techniques, and instruments used during morphological data production. In other words, it's purpose is to provide a publicly available resource for recording and documenting morphological metadata. Moreover, it is also a repository for different types of media files that can be uploaded in order to serve as support and empirical substantiation of the results of morphological investigations. Our long-term perspective with Morph·D·Base is to provide an instrument that will enable a highly formalized and standardized way of generating morphological descriptions using a morphological ontology that will be based on the web ontology language (OWL - http://www.w3.org/TR/owl-features/). This, however, represents a project that is still in development.

Human Autophagy Database

HADb

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HADb provides a complete and an up-to-date list of human genes and proteins involved directly or indirectly in autophagy as described in literature.

mentha

the interactome browser

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mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate "the interactome". mentha's approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. mentha offers eight interactomes (Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli K12, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae) plus a global network that comprises every organism, including those not mentioned. The website and the graphical application are designed to make the data stored in mentha accessible and analysable to all users. Source databases are: MINT, IntAct, DIP, MatrixDB and BioGRID.

Mammalian Transcriptomic Database

MTD

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MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features.

HIstome

The Histone Infobase

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HIstome: The Histone Infobase is a database of human histones, their post-translational modifications and modifying enzymes. HIstome is a combined effort of researchers from two institutions, Advanced Center for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai and Center of Excellence in Epigenetics, Indian Institute of Science Education and Research (IISER), Pune.

MiCroKitS

formerly: MiCroKit

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During cell cycle, numerous proteins temporally and spatially localized in distinct sub-cellular regions including centrosome (spindle pole in budding yeast), kinetochore/centromere, cleavage furrow/midbody (related or homolog structures in plants and budding yeast called as phragmoplast and bud neck, respectively), telomere and spindle spatially and temporally. These sub-cellular regions play important roles in various biological processes. In this work, we have collected all proteins identified to be localized on kinetochore, centrosome, midbody, telomere and spindle from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musculus and H. sapiens based on the rationale of "Seeing is believing" (Bloom K et al., 2005). Through ortholog searches, the proteins potentially localized at these sub-cellular regions were detected in 144 eukaryotes. Then the integrated and searchable database MiCroKiTS - Midbody, Centrosome, Kinetochore, Telomere and Spindle has been established.

Harvard Medical School, Library of Integrated Network-Based Cellular Signatures Database

HMS, LINCS database

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The Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.

The Taenia solium Genome Project

T. solium Genome Project

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>>>!!!<<< 2021-08; The repository is no longer available. >>>!!!<<< Archived page of Taenia solium genome project see https://web.archive.org/web/20160309194611/http://www.taeniasolium.unam.mx/taenia

The MaxQuant DataBase

MaxQB

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MaxQB stores and displays collections of large proteomics projects and allows joint analysis and comparison. As a first dataset is contains proteome data of 11 different human cell lines. The 11 cell line proteomes together identify proteins expressed from more than half of all human genes. For each protein of interest, expression levels estimated by label-free quantification can be visualized across the cell lines. Similarly, the expression rank order and estimated amount of each protein within each proteome are plotted.

Small Molecule Pathway Database

formerly: PathBank

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The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.

Physical mapping data at Canada's Michael Smith Genome Sciences Centre - Data

Physical Mapping Data Access

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FPC Mapping data files from species that have been fingerprinted at Canada's Michael Smith Genome Sciences Centre (BCGSC).

The Human Protein Atlas

HPA

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The Swedish Human Protein Atlas project has been set up to allow for a systematic exploration of the human proteome using Antibody-Based Proteomics. This is accomplished by combining high-throughput generation of affinity-purified antibodies with protein profiling in a multitude of tissues and cells assembled in tissue microarrays. Confocal microscopy analysis using human cell lines is performed for more detailed protein localization. The program hosts the Human Protein Atlas portal with expression profiles of human proteins in tissues and cells. The main objective of the resource centre is to produce specific antibodies to human target proteins using a high-throughput production method involving the cloning and protein expression of Protein Epitope Signature Tags (PrESTs). After purification, the antibodies are used to study expression profiles in cells and tissues and for functional analysis of the corresponding proteins in a wide range of platforms.

PlasmID

Plasmid Information Database

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<<<!!!<<< As of Aug. 15, 2019, we are suspending plasmid distribution from the collection. If you would like to request BioPlex ORF clones (Harper lab) or if you identify other clones in our collection for which you cannot find an alternative, please email us at plasmidhelp@hms.harvard.edu. >>>!!!>>>