Links M-Z

  • MalaCards DATABASE | ANNOTATION – GENOMICS – SYSTEMS BIOLOGY
  • MalaCards is an integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes. The MalaCards disease and disorders database is organized into “disease cards”, each integrating prioritized information, and listing numerous known aliases for each disease, along with a variety of annotations, as well as inter-disease connections, empowered by the GeneCards relational database, searches, and GeneAnalytics set-analyses. Annotations include: symptoms, drugs, articles, genes, clinical trials, related diseases/disorders and more. An automatic computational information retrieval engine populates the disease cards, using remote data, as well as information gleaned using the GeneCards platform to compile the disease database. The MalaCards disease database integrates both specialized and general disease lists, including rare diseases, genetic diseases, complex disorders and more.

  • MassBank DATABASE | METABOLISM
  • MassBank is a mass spectral database of experimentally acquired high resolution MS spectra of metabolites.

  • MBRole (article) DATABASE | ANNOTATION – PHARMACOLOGY
  • MBRole performs overrepresentation (enrichment) analysis of categorical annotations for a set of compounds of interest. These categorical annotations correspond to biological and chemical information available in a number of public databases and software. Current annotations include: Biological annotations (Pathways (from KEGG and SMPDB); Enzyme interactions (from KEGG); Other interactions (from KEGG); Diseases (from HMDB); Tissue, biofluid and cellular location (from HMDB); Pharmacological action (from PubChem); Biological role, chemical role and application (from ChEBI and KEGG)) and Chemical annotations (Chemical taxonomy (from HMDB) and Chemical groups (from Checkmol)).

  • MDL Toxicity Database (commercial) DATABASE | TOXENDPOINT
  • The Toxicity Database includes the complete contents of the Registry of Toxic Effects of Chemical Substances database (US Centers for Disease Control and Prevention), the GEN-TOX database (US Environmental Protection Agency) and the Chemical Carcinogenesis Research Information System database (National Cancer Institute). A structure-searchable bioactivity database of toxic chemical substances containing data from in vivo and in vitro studies.

  • MedDRA THESAURI | ADVERSE EVENT
  • The Medical Dictionary for Regulatory Activities (MedRA) is a medical terminology used to classify adverse event information associated with the use of biopharmaceuticals and other medical products (e.g., medical devices and vaccines). Coding these data to a standard set of MedDRA terms allows health authorities and the biopharmaceutical industry to more readily exchange and analyze data related to the safe use of medical products. The European Medicines Agency has required that all serious adverse event reports be submitted electronically, using MedDRA codes, since January 2003.

  • MEDIC (article) MEDIC-Slim disease categories THESAURI
  • CTD biocurators undertook a novel initiative to map the flat list of OMIM disease terms into the hierarchical nature of the MeSH vocabulary. The result is CTD’s ‘merged disease vocabulary’ (MEDIC), a unique resource that integrates OMIM terms, synonyms and identifiers with MeSH terms, synonyms, definitions, identifiers and hierarchical relationships. MEDIC is both a deep and broad vocabulary, composed of 9700 unique diseases described by more than 67 000 terms (including synonyms). It is freely available to download in various formats from CTD.

    On October 2012, CTD released its MEDIC-Slim disease categories and a new filtering tool that adds functionality, reduces complexity of disease information, and eases data management. To annotate disease information at CTD, biocurators use MEDIC, a hierarchical disease controlled vocabulary that merges MeSH and OMIM disease terms into a single resource. CTD has now generated ‘MEDIC-Slim’, a high-level set of terms that organize all 9,700 MEDIC diseases into 36 generic categories. These
    mappings to MEDIC-Slim are available on all CTD “Disease” pages and can be downloaded from the MEDIC files. Currently, CTD contains data for over 6,000 diseases, including more than 200,000 direct chemical-disease and gene-disease interactions, and 12 million inferred relationships (http://ctdbase.org/about/dataStatus.go). To help manage this knowledge, users can now filter disease information using MEDIC-Slim categories. For example, the environmental chemical bisphenol A is associated with over 2,000 unique diseases at CTD (http://ctdbase.org/detail.go?type=chem&acc=C006780&view=disease). A pop-up chart conveniently shows the distribution of bisphenol A to the 36 disease categories. A user interested in exploring how this chemical is linked to cardiovascular diseases can select that category from either the graph directly (by clicking on the bar) or using the pick-list in the “Disease Category” filter (below the chart) to retrieve the annotations relevant to that disease filter. MEDIC-Slim allows similar types of diseases to be grouped and analyzed for meta-analysis, provides better visualization opportunities, and facilitates knowledge management for users of CTD.

  • MEMOSys TOOL | METABOLISM
  • Metabolic Model System (MEMOSys) is a web based bioinformatics platform for the management, storage, and development of metabolic models. It supports the development of new models by providing a built in version control system which offers access to the complete reconstruction history. Moreover, the integrated web board, the fine-grained authorization system, and the definition of user roles allow collaborations across departments and universities. Research on existing models is facilitated by a powerful search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. The web application is based on the Java EE framework and offers an intuitive user interface. It currently contains several well annotated and publicly available models.

  • mentha (article) DATABASE | SYSTEMS BIOLOGY
  • mentha is a PPI resource that takes advantage of the recent establishment of the International Molecular Exchange (IMEx)1 consortium and the development of the Proteomics Standard Initiative Common Query Interface (PSICQUIC)2 for automatic access to molecular-interaction databases. mentha integrates protein-interaction data curated by experts in compliance with IMEx curation policies, using the PSICQUIC protocol to implement an automatic procedure that, every week, without human intervention, aligns the integrated database with data regularly annotated by the primary databases.

  • MESSI (article) TOOL | METABOLISM – PATHWAYS
  • Metabolic Engineering target Selection and best Strain Identification tool (MESSI) is a web server for predicting efficient chassis and regulatory components for yeast bio-based production. The server provides an integrative platform for users to analyse ready-to-use public high-throughput metabolomic data, which are transformed to metabolic pathway activities for identifying the most efficient S. cerevisiae strain for the production of a compound of interest. As input MESSI accepts metabolite KEGG IDs or pathway names. MESSI outputs a ranked list of S. cerevisiae strains based on aggregation algorithms.

  • Metab2MeSH (article) THESAURI
  • Metab2MeSH uses a statistical approach to reliably and automatically annotate compounds with the concepts defined in MeSH, the National Library of Medicine’s controlled vocabulary for biology and medicine. The Metab2MeSH web application searches compounds or MeSH terms and displays resulting pairs of compounds and MeSH terms that match the search term. The compounds / MeSH term pairs displayed are those that are significantly associated in PubMed abstracts and are ordered highest to lowest by significance score.

  • MetaboLights DATABASE | METABOLISM
  • MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. We will provide search services around spectral similarities and chemical structures.

  • Metabolites in Safety Testing OTHER | METABOLISM – TOXENDPOINT
  • An special issue of Chemical Research in Toxicology journal devoted to Metabolites in Safety Testing (MIST).

  • MetaboNetworks (article) TOOL | METABOLISM
  • A Matlab-based tool to create custom sub-networks using main substrate-product pairs as defined by the Kyoto Encyclopaedia of Genes and Genomes (KEGG). It can be used to explore transgenomic interactions, for example mammalian and bacterial associations. It calculates the shortest path between a set of metabolites (e.g. biomarkers from a metabonomic study) and plots the connectivity between metabolites as links in a network graph. The resulting graph can be changed and explored interactively. Furthermore, nodes in the graph are linked to the KEGG compound webpage. A multi-systemic example data set is provided of a supra-organism, this includes reactions that can occur in compartments of homo sapiens, firmicutes and/or bacretoidetes species. The MetaboGetworks function can be used to generate custom multi-organism databases to use in the MetaboNetworks function.

  • MetaCyc (article) DATABASE | METABOLISM
  • MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1500 pathways from more than 2000 different organisms [more], and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes.

  • MetaDrug™ (commercial) DATABASE | GENOMICS – PHARMACOLKINETICS – PHARMACOLOGY
  • MetaDrug™ is a unique systems pharmacology platform designed for evaluation of biological effects of small molecule compounds on the human body, with bioinformatics applications from toxicogenomics to translational medicine. MetaDrug™ helps to solve such problems as drug’s mechanism of action, toxicity and off-target effects, deduced from the structure and any kind of supplementary toxicogenomics data. The product is intended to be used by medicinal chemists and biologists active in pre-clinical areas of high content and high throughput screening, bioassays, hit-to-lead libraries, lead optimization, PK and toxicogenomics, with the eventual goal being practical applications in translational medicine and more. Applications: Drug repositioning,Compound prioritization and library triage, Compound profiling, Hit-to-lead optimization, Drug comparison to competitor’s, Toxicogenomics studies.

  • MetaMap (article) TOOL | METABOLISM – NETWORK
  • MetaMapp is a tool to construct metabolomics network graphs from the chemical similarity and mass spectral similarity matrices and the KEGG reaction pair database. It facilitates the visualization of statistical output to enable the biological interpretation of underlying data trends and patterns.

  • MetaPath (article) TOOL | METABOLISM
  • A searchable information management system for the metabolism information including complete metabolic maps, experimental conditions, biotransformations, enzymatic system, rates and identified metabolites.

  • MetaRanker 2.0 (article) TOOL | SYSTEMS BIOLOGY – TEXT MINING
  • MetaRanker 2.0 is a web server for prioritization of common and rare frequency genetic variation data. Based on heterogeneous data sets including genetic association data, protein-protein interactions, large-scale text-mining data, copy number variation data and gene expression experiments, MetaRanker 2.0 prioritizes the protein-coding part of the human genome to shortlist candidate genes for targeted follow-up studies.

  • METLIN DATABASE | METABOLISM
  • METLIN is a metabolite database for metabolomics containing over 25,000 structures, it is also represents a data management system designed to assist in a broad array of metabolite research and metabolite identification by providing public access to its repository of current and comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available on the METLIN website. Each metabolite is conveniently linked to outside resources such as the the Kyoto Encyclopedia of Genes and Genomes (KEGG) for further reference and inquiry. MS and MS data is also available on many of the metabolites. The list is expanding continuously as more metabolite information is being deposited and discovered.

  • MGI DATABASE | GENOMICS – PHARMACOLOGY
  • The MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

  • MoKa TOOL | ADME – QSAR MODELING – STRUCTURE-BASED PREDICTION
  • Accurate pK prediction and automatic structure modification is critical for many computational chemistry methods which are strongly dependent on the tautomerization and protonation state of the structures, including docking, binding affinity estimation, QSAR and ADME modelling, and metabolism prediction. MoKa implements a novel approach for in silico computation of pKa values; trained using a very diverse set of more than 25000 pKa values, it provides accurate and fast calculations using an algorithm based on descriptors derived from GRID molecular interaction fields.

    Kibitzer
    is an automatic and expert tool to expand the MoKa internal database with a corporate database of pKa values. A fully automated training procedure makes it easy to create customized pKa models by using your experimental pKa values. You can also easily import an SD file containing experimental pKa values into the Kibitzer tool. Check the pKa assignments and, if necessary, correct them by using the embedded molecular viewer. Create customized models and verify the enhancements using MoKa.

  • MPD (article) DATABASE | SYSTEMS BIOLOGY
  • The Mouse Phenome Database (MPD; http://phenome.jax.org). MPD houses a wealth of strain characteristics data to facilitate the use of the laboratory mouse in translational research for human health and disease, helping alleviate problems involving experimentation in humans that cannot be done practically or ethically. Data sets are voluntarily contributed by researchers from a variety of institutions and settings, or in some cases, retrieved by MPD staff from public sources. MPD maintains a growing collection of standardized reference data that assists investigators in selecting mouse strains for research applications; houses treatment/control data for drug studies and other interventions; offers a standardized platform for discovering genotype-phenotype relationships; and provides tools for hypothesis testing. MPD improvements and updates since our last NAR report are presented, including the addition of new tools and features to facilitate navigation and data mining as well as the acquisition of new data (phenotypic, genotypic and gene expression).

  • MSigDB DATABASE | GENOMICS
  • The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can: search for gene sets by keyword; browse gene sets by name or collection; examine a gene set and its annotations; download gene sets and investigate gene sets (Compute overlaps between your gene set and gene sets in MSigDB, Categorize members of a gene set by gene families. or View the expression profile of a gene set in any of the three provided public expression compendia).

  • MSRD (article) TOOL | METABOLISM
  • The Metabolite Route Search and Design (MRSD) is a tool developed for predict and design route based on the weighted compound transform diagraph. The search submodule returns text-like routes between a source and product compound within seconds in the network of one or multiple organisms based on data from KEGG. The design submodule designs a route from an appointed compound in an interactive way. The direction of the design can be forward which means starting from a source compound, and backward which means ending with a product compound.

  • MutAIT (article) DATABASE – TOOL | GENOTOXICITY – RISK ASSESSMENT
  • The Mutation Analysis Informatics Tools (MutAIT) is a new genetic toxicology portal that provides easy access to two of the largest genetic toxicology databases, the Mammalian Gene Mutation Database (MGMD) and TransgenicDB. TransgenicDB is a comprehensive collection of transgenic rodent mutation data initially compiled and collated by Health Canada. The updated MGMD contains approximately 50 000 individual mutation spectral records from the published literature. The portal not only gives access to an enormous quantity of genetic toxicology data, but also provides statistical tools for dose-response analysis and calculation of benchmark dose.

  • myChEMBL (article) TOOL | PHARMACOLOGY
  • myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications.Availability and implementation: The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current.

  • MyMiner (article) THESAURI – TOOL | ANNOTATION
  • MyMiner provides tools and methods for researchers to easily and rapidly classify scientific documents or biomedical terms. This application has been developed with the following ambitious goals: to speed up the process of information transfer from scientific literature to computationally exploitable data; to facilitate the comparison and the evaluation of dataset sets of biological documents. The definition of high quality reference datasets will in turn improve machine learning technique predictions; to allow researchers to define topic-specific databases; to serve, promote and facilitate community annotation efforts. MyMiner application integrates several distinct tools and options which contributes to a better and easier classification.

  • NAT Gene Nomenclature THESAURI | METABOLISM – PHARMACOLOGY
  • This resource offers compilation of the Human Arylamine N-Acetyltransferase (NAT) Gene Nomenclature.

  • NCBO Bioportal (article) THESAURI – TOOL | ANNOTATION – ONTOLOGY
  • BioPortal 2.5 is a Web-based platform for browsing, visualizing, mapping, and commenting on biomedical ontologies and terminologies. Use BioPortal to access and share ontologies that are actively used in biomedical communities. You can search for terms in ontologies (try typing “Melanoma” in the “Search all ontologies” box in the left column), browse a list of ontologies in BioPortal (type “NCI THESAURI” in the “Find an ontology” box in the middle column), search biomedical resources that we automatically annotated with ontology terms (try typing “Melanoma” in the “Search resources” box in the right column). You can create ontology-based annotations for your own text, link your own project that uses ontologies to the description of those ontologies; find and create relations between terms in different ontologies; review and comment on ontologies and their components as you browse them. Sign in to BioPortal to submit a new ontology or ontology-based project, provide comments on ontologies or add ontology mappings.

  • NCGC glossary THESAURI
  • Glossary of Quantitative Biology Terms by Eli Lilly and Company and the National Institutes of Health Chemical Genomics Center.

  • NCTRlcdb DATABASE | GENOMICS – QSAR MODELING – TOXENDPOINT
  • A National Center for Toxicological Research liver cancer database (NCTRlcdb) containing 999 chemicals has been developed based on liver-specific carcinogenicity. This database was constructed with the assumption that organ-specific carcinogenicity is a cleaner endpoint for building a biological predictive model. The NCTRlcdb benefits FDA reviewers by: Facilitating the construction of cleaner and better carcinogenicity models by FDA and other organizations thus providing a means to rapidly predict carcinogenicity to aid in evaluating new chemicals submitted for approval. Serving as a prototype for other organ-specific carcinogenicity databases for better Quantitative Structure-Activity Relationships (QSAR) and toxicogenomics model prediction. In the NCTRlcdb, each chemical was assigned one of the following toxicity classifications based on studies of male and female mice and rats: a) liver carcinogen (273), b) other carcinogen (293), c) non-carcinogen (304) and d) other (129).

  • NetPredATC (article) TOOL | ANNOTATION- PHARMACOLOGY
  • NetPredATC aims to assign drug’s potential ATCcodes by integrating chemical structures and target proteins. Theit method was validated on four drug datasets with various target proteins, including enzymes, ion channels, G-protein couple receptors and nuclear receptors.

  • Nonclinical Data Interconnectivity for Endpoint Predictivity PROJECT | TOXENDPOINT
  • The Nonclinical Data Interconnectivity for Endpoint Predictivity (NICE) project is derived from the combination of 2 former projects in the Nonclinical WG: Endpoint Predictivity and Data Interconnectivity as a FDA-PhUSE initiative.

  • NTP PROJECT | TOXENDPOINT
  • The National Toxicology Program (NTP) is an interagency program whose mission is to evaluate agents of public health concern by developing and applying tools of modern toxicology and molecular biology. The program maintains an objective, science-based approach in dealing with critical issues in toxicology and is committed to using the best science available to prioritize, design, conduct, and interpret its studies. To that end, the NTP is continually evolving to remain at the cutting edge of scientific research and to develop and apply new technologies. (See Study Results & Research Project)

  • NTP Evaluation of In Vitro Cytotoxicity Test Methods DATABASE | TOXENDPOINT
  • Data from 347 Chemicals for the Calculation of the Regression Between Cytotoxicity and Acute Oral Systemic Toxicity.

  • OBO Foundary PROJECT – THESAURI | ONTOLOGY
  • The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. In addition to a listing of OBO ontologies, they also provide a statement of the OBO Foundry principles, discussion fora, technical infrastructure, and other services to facilitate ontology development.

  • OBO-Edit THESAURI – TOOL | ANNOTATION – ONTOLOGY
  • OBO-Edit is an open source ontology editor written in Java optimized for the OBO biological ontology file format. It features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities. This is the required editor to read the Anatomy Ontology file from the Ontology Development Progress report of eTOX.

  • OCHEM DATABASE | ADME
  • The QSPR website provides free on-line access to physico-chemical, ADME/T and different biological activities of molecules. It is organized in Wiki style and the users can upload, store, access, organise and edit data directly on the WWW.

  • OECD REGULATORY GUIDELINES | QSAR MODELING
  • The Organization for Economic Co-operation and Development (OECD) facilitates practical application of (Q)SAR approaches in regulatory contexts by governments and industry and improves their regulatory acceptance. The OECD (Q)SAR Project has developed various outcomes such as the principles for the validation of (Q)SAR models, guidance documents as well as the (Q)SAR Application Toolbox. The OECD (Q)SAR Project is carried out with the financial assistance of the European Union.
    2nd OECD’s Guidance on Grouping Chemicals for hazard assessment (April 2014).

  • OLSVis (article) THESAURI – TOOL | ONTOLOGY
  • OLSVis (“oh-el-es vis”) is an interactive visualisation of EBI’s Ontology Lookup Service (OLS). It is an application of WordVis’ visualiser (see also WordVis’ page). OLSVis visualises the contents of the publicly available OLS-data. OLS is a combination of several biomedical ontologies. These are ‘official’ terminology lists (often hierarchies) that are used to unambiguously describe and share information on various biological topics. The OLS database is updated weekly. OLSVis detects this usually within a few hours and updates automatically as well.

  • OMICtools (article) DATABASE – TOOL | ANNOTATION – GENOMICS – METABOLISM – ONTOLOGY – SYSTEMS BIOLOGY – TEXT MINING – RISK ASSESSMENT
  • OMICtools is a workflow for genomic, transcriptomic, proteomic, and metabolomic data analysis. All tools have been classified by omic technologies (NGS, microarray, PCR, MS, NMR), applications and analytical steps.

  • omniBiomarker (article) TOOL | BIOMARKER
  • omniBiomarker, a web-based application that uses knowledge from the NCI Cancer Gene Index to guide the selection of biologically relevant algorithms for identifying biomarkers.

  • OntoCAT (article) THESAURI – TOOL | ONTOLOGY
  • OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including EBI Ontology Lookup Service (OLS) and NCBO BioPortal, as well as user-specified local ontology files in OWL and OBO (via OWL API). Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. OntoCAT exists in many flavours including a stand-alone database and browser, REST service, google app application and ontoCAT R package to work with ontologies in R environment. See download page for package download options. OntoCAT is open source and is available under the LGPLv3 license. Releases are often and comprehensively tested, so the end user does not have to worry about the updates in access to underlying resources.

  • Ontodog (article) TOOL | ANNOTATION – TEXT MINING
  • Ontodog is a web-based system that can generate an ontology subset based on Excel input, and support generation of an ontology community view, which is defined as the whole or a subset of the source ontology with user-specified annotations including user-preferred labels. Ontodog allows users to easily generate community views with minimal ontology knowledge and no programming skills or installation required. Currently >100 ontologies including all OBO Foundry ontologies are available to generate the views based on user needs.

  • OntoDT (article) TOOL | ONTOLOGY
  • OntoDT is a generic ontology for the representation of scientific knowledge about datatypes. OntoDT defines basic entities, such as datatype, properties of datatypes, specifications, characterizing operations, and a datatype taxonomy.

  • ontogrator THESAURI – TOOL | ONTOLOGY
  • ontogrator is a web application that demonstrates how ontologies can be used to automatically generate user interfaces for browsing data sets.

  • Ontology Adverse Events (article) THESAURI – TOOL | ONTOLOGY
  • Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention.

  • Ontology Lookup Service THESAURI – TOOL | ONTOLOGY
  • The Ontology Lookup Service (OLS) is a spin-off of the PRIDE project, which required a centralized query interface for ontology and controlled vocabulary lookup. While many of the ontologies queriable by the OLS are available online, each has its own query interface and output format. The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format.The OLS can integrate any ontology available in the Open Biomedical Ontology (OBO) format.

  • OntoMaton (article) THESAURI – TOOL | ONTOLOGY
  • OntoMaton is an open source solution that brings ontology lookup and tagging capabilities into a cloud-based collaborative editing environment, harnessing Google Spreadsheets and the NCBO Web services. It is a general purpose, format-agnostic tool that may serve as a component of the ISA software suite. OntoMaton can also be used to assist the ontology development process.

  • Open Data Handbook OTHER
  • This handbook discusses the legal, social and technical aspects of open data. It can be used by anyone but is especially designed for those seeking to open up data. It discusses the why, what and how of open data – why to go open, what open is, and the how to ‘open’ data.

  • Open PHACTS PROJECT | PHARMACOLOGY
  • Open PHACTS is an Innovative Medicines Initiative project aiming to deploy a highly innovative open standards, open access, semantic web approach to address key bottlenecks in small molecule drug discovery – disparate information sources, lack of standards and information overload. It will become an open, integrated and sustainable chemistry, biology and pharmacology knowledge resource for drug discovery. It will provide tools for a comprehensive platform of chemical, biological and pharmacological information, confederated from vast, distributed and variable data and information sources. This semantically enriched and fully interoperable platform will deliver information on small molecules and their pharmacological profiles, including pharmacokinetics and ADMET data as well as on biological targets and pathways. The proposed platform will be a widely accessible, open innovation platform that will serve EFPIA partners as well as biotech and academic drug-discovery for one of their core business activities: knowledge discovery and verification. Practising drug-discovery scientists in both the public and the private sector will turn to this service to: – integrate data on target expression, biological pathways and pharmacology to identify the most productive points for therapeutic intervention – investigate the in vitro pharmacology and mode-of-action of novel targets to help develop screening assays for drug discovery programs – compare molecular interaction profiles to assess potential off-target effects and safety pharmacology – analyse chemical motifs against biological effects to deconvolute high content biology assays. Join to their Linkedin group or follow them at their Twitter account.

  • Open PHACTS Explorer TOOL | PHARMACOLOGY
  • The Open PHACTS Explorer allows multiple sources of publicly-available pharmacological and physicochemical data to be intuitively queried, and makes data provenance accessible at every step. The Open PHACTS Explorer was built to answer critical pharmacological questions as defined by academic and pharmaceutical industry scientists.

  • openBIS (article) TOOL | WORKFLOW
  • openBIS is an open, distributed system for managing biological information. The main goal is to support biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: High Content Screening, Proteomics, Deep Sequencing, and Metabolomics.

  • OpenFDA DATABASE | SYSTEMS BIOLOGY
  • OpenFDA is an exciting new initiative in the Food and Drug Administration’s Office of Informatics and Technology Innovation spearheaded by FDA’s Chief Health Informatics Officer. OpenFDA offers easy access to FDA public data and highlight projects using these data in both the public and private sector to further regulatory or scientific missions, educate the public, and save lives.

  • OpenTox PROJECT | ONTOLOGY – QSAR MODELING – TOXENDPOINT
  • The Open Source Predictive Toxicology Framework (OpenTox) was funded under the EU FP 7: HEALTH-2007-1.3-3 Promotion, development, validation, acceptance and implementation of QSARs (Quantitative Structure-Activity Relationships) for toxicology, Project Reference Number Health-F5-2008-200787 (2008-2011). Their goal is to develop an interoperable predictive toxicology framework which may be used as an enabling platform for the creation of predictive toxicology applications.

  • OpenTox Workshop Sept-10 OTHER
  • Development and Use of Predictive Toxicology Applications. Presentation slides used by Barry Hardy, Christoph Helma, Nina Jeliazkova, Olga Tcheremenskaia, Stefan Kramer, Haralambos Sarimveis and Andreas Karwath on their presentation of the OpenTox Framework at the OpenTox workshop held 19 September 2010, Rodos Palace Hotel, Rhodes, Greece.

  • OPSIN (article) THESAURI – TOOL | PHARMACOLOGY
  • The Open Parser for Systematic IUPAC Nomenclature (OPSIN) algorithm interprets the majority of organic chemical nomenclature in a fast and precise manner using an approach based on a regular grammar to guide tokenization, a potentially difficult problem in chemical names. From the parsed chemical name, an XML parse tree is constructed that is operated on in a stepwise manner until the structure has been reconstructed from the name. This software can serve as the basis for future open source developments of chemical name interpretation.

  • Oscar3 THESAURI – TOOL | PHARMACOLOGY
  • Oscar3 is a tool for shallow, chemistry-specific parsing of chemical documents. It identifies (or attempts to identify) chemical names (singular nouns, plurals, verbs etc., also formulae and acronyms, some enzymes and reaction names). In addition, where possible the chemical names that are detected are annotated with structures, either via lookup or name-to-structure parsing (“OPSIN”), and with identifiers from the chemical ontology ChEBI.

  • OSIRIS PROJECT – REGULATORY GUIDELINES
  • The goal of the project OSIRIS was to develop integrated testing strategies (ITS) fit for REACH that enable to significantly increase the use of non-testing information for regulatory decision making, and thus to minimise the need for animal testing. To this end, operational procedures were developed, tested and disseminated that guide a transparent and scientifically sound evaluation of chemical substances in a risk-driven, context-specific and substance-tailored manner.

  • OTO (article) THESAURI – TOOL | ONTOLOGY – TEXT MINING
  • Ontology Term Organizer (OTO) is a user-friendly, web-based, consensus-promoting, open source application for organizing domain terms by dragging and dropping terms to appropriate locations. The application is designed for users with specific domain knowledge such as biology but not in-depth ontology construction skills. Specifically OTO can be used to establish is_a, part_of, synonym, and order relationships among terms in any domain that reflects the terminology usage in source literature and based on multiple experts opinions.

  • OwlExporter (article) THESAURI – TOOL | ONTOLOGY
  • The OwlExporter is a tool designed to automate the process of ontology export from text.

  • PaDEL-DDPredictor (article) TOOL | ADME
  • The PaDEL-DDPredictor is a software to calculate pharmacodynamics, pharmacokinetics and toxicological properties of compounds.

  • PALLAS TOOL | MOLECULAR DESCRIPTORS
  • PALLAS for WINDOWS is a software to predict pKa, logP, logD values and metabolites based on structural formulae of compounds.

  • PAPi (article) TOOL | METABOLISM – PATHWAY
  • The algorithm Pathway Activity Profiling (PAPi) provides comparison between metabolic pathway activities from metabolite profiles using the metabolite profile and KEGG database to correlate metabolomics datasets and metabolic pathways activities in a high-throughput way.

  • PASS online (article) TOOL | ENZYMES – PHARMACOLOGY – SOFTWARE – SYSTEMS BIOLOGY – TRANSPORTERS
  • PASS Online predicts over 4000 kinds of biological activity, including pharmacological effects, mechanisms of action, toxic and adverse effects, interaction with metabolic enzymes and transporters, influence on gene expression, etc.

  • PathCase-MAW DATABASE | METABOLISM
  • The PathCase-MAW Database captures the multi-tissue/multi-compartment nature of the metabolic network and the architecture.
    As of now, it contains: 26 Metabolic Pathways, 282 Biological Processes (Reactions), and 243 Basic Molecules.

  • PATHTEXT2 (article) TOOL | PATHWAYS – TEXT MINING
  • .

  • PathwayBooster TOOL – DATABASE | METABOLISM – PATHWAYS
  • PathwayBooster is an open-source software tool to support the comparison and curation of metabolic models. It combines gene annotations from GenBank files and other sources with information retrieved from the metabolic databases BRENDA and KEGG to produce a set of pathway diagrams and reports summarising the evidence for the presence of a reaction in a given organism’s metabolic network. By comparing multiple sources of evidence within a common framework, PathwayBooster assists the curator in the identification of likely false positive (misannotated enzyme) and false negative (pathway hole) reactions. Reaction evidence may be taken from alternative annotations of the same genome and/or a set of closely related organisms.

  • PathwaysWeb (article) DATABASE | PATHWAYS – SYSTEMS BIOLOGY
  • PathwaysWeb is a resource-based, well-documented web system that provides publicly available information on genes, biological pathways, Gene Ontology (GO) terms, gene-gene interaction networks (importantly, with the directionality of interactions) and links to key-related PubMed documents. The PathwaysWeb API simplifies the construction of applications that need to retrieve and interrelate information across multiple, pathway-related data types from a variety of original data sources. PathwaysBrowser is a companion website that enables users to explore the same integrated pathway data. The PathwaysWeb system facilitates reproducible analyses by providing access to all versions of the integrated datasets. Although its GO subsystem includes data for mouse, PathwaysWeb currently focuses on human data.

  • PatientsLikeMe DATABASE | PHARMACOLOGY
  • PatientsLikeMe is a privately funded company dedicated to making a difference in the lives of patients diagnosed with life-changing diseases and it is committed to providing a better, more effective way to capture valuable results and share them with patients, healthcare professionals, and industry organizations that are trying to treat the disease.

  • PAV ontology (article)THESAURI – TOOL | ONTOLOGY
  • The PAV ontology is a provenance, authoring and versioning namespace, a lightweight ontology for capturing “just enough” descriptions essential for tracking the provenance, authoring and versioning of web resources. PAV distinguishes between contributors, authors and curators of content and creators of representations in addition to the provenance of originating resources that have been accessed, transformed and consumed..

  • pCEC (article) DATABASE | GENOMICS – TOXENDPOINT
  • The profiles of Chemical Effects on Cells is a toxicogenomics database with a system of classifying chemicals that have effects on human health. This system classifies chemicals that act on the cell from the viewpoint of gene expression signatures. This database stores and handles gene expression profiling information and the categorizations of toxicity data, and separates chemicals into a variety groups by the type of influence. The gene expression profiling was achieved by the self-organizing maps (SOM) technique, and the toxicity data are shown using minimum spanning tree (MST) algorithms.

  • PDBwiki (article) TOOL | PHARMACOLOGY
  • PDBWiki, a scientific wiki for the community annotation of protein structures. The wiki consists of one structured page for each entry in the the Protein Data Bank (PDB) and allows the user to attach categorized comments to the entries. Additionally, each page includes a user editable list of cross-references to external resources. As in a database, it is possible to produce tabular reports and ‘structure galleries’ based on user-defined queries or lists of entries. PDBWiki runs in parallel to the PDB, separating original database content from user annotations. PDBWiki demonstrates how collaboration features can be integrated with primary data from a biological database. It can be used as a system for better understanding how to capture community knowledge in the biological sciences. For users of the PDB, PDBWiki provides a bug-tracker, discussion forum and community annotation system.

  • PESCADOR (article) TOOL | NETWORK
  • The Platform for Exploration of Significant Concepts AssociateD to co-Occurrences Relationships (PESCADOR), is a web tool that extracts a network of interactions from a set of PubMed abstracts given by a user, and allows filtering the interaction network according to user defined concepts.

  • PharmaADME DATABASE | ADME – BIOMARKER
  • This industry initiated effort was launched to develop a consensus, “Core List” of standardized “evidence based” drug metabolizing (ADME) genetic biomarkers that are broadly applicable to many pharmaceutical clinical trials and FDA drug submissions. The effort was driven by a unique multidisciplinary group of representatives from the pharmaceutical industry and an academic center. Our goal was to develop a list of genes and geneticbiomarkers that could be screened using today’s technology platforms to identify predictors of pharmacokinetic variability that could impact drug safety and efficacy in the current drug development process. Through a phased process and using pre-defined criteria, the group identified a “Core List” of 32 ADME genes, which includes 184 markers that can be used to screen subjects in clinical trials. This work has become the basis for two different commercially available assays and complete information can be found on the ADME Core gene and marker list on this site.

  • PharmaPendium DATABASE | DRUG SAFETY – PHARMACOKINETICS – RISK ASSESSMENT
  • Pharmapendium is the only online resource able to search all FDA/CDER/FOI archived FDA drug approval review and correspondence documentation since 1938, as well as an EMA EPAR approval document database, PharmaPendium gives you unrivalled insights into the entire history of drug development. PharmaPendium informs your critical pipeline decisions and speeds up the drug development and approval process by making it easy to retrieve comparative preclinical and clinical drug efficacy, safety and pharmacokinetics information in regulatory, scientific and commercial contexts.

  • PharmGKB DATABASE | PHARMACOLOGY – PATHWAY
  • PharmGKB has the mission to collect, encode, and disseminate knowledge about the impact of human genetic variations on drug response. We curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways.

  • PhenoHM (article) DATABASE | GENOMICS
  • PhenoHM is a human-mouse comparative phenome-genome server that facilitates cross-species identification of genes associated with orthologous phenotypes. Combining and extrapolating the knowledge about the roles of individual gene functions in the determination of phenotype across multiple organisms improves our understanding of gene function in normal and perturbed states and offers the opportunity to complement biologically the rapidly expanding strategies in comparative genomics.

  • Phenotype RCN PROJECT | SYSTEMS BIOLOGY
  • The Phenotype Ontology Research Coordination Network (RCN) was funded by NSF to establish a network of scientists who are interested in comparing phenotypes across species and in developing the tools and methods needed in making this possible.

  • PhUSE PROJECT -TOOL
  • The Pharmaceutical Users Software Exchange (PhUSE) is an Independent, Not-for-profit organization run by volunteers. Since its inception, PhUSE has expanded from its roots as a conference for European Statistical Programmers, to a global platform for the discussion of topics encompassing the work of Data Managers, Biostatisticians, Statistical Programmers and eClinical IT professionals.

  • PHYSPROP DATABASE | ADME – MOLECULAR DESCRIPTORS
  • The Physical Properties Database (PHYSPROP) contains chemical structures, names, and physical properties for over 41,000 chemicals. Physical properties are collected from a wide variety of sources, and include experimental, extrapolated, and estimated values for melting point, boiling point, water solubility, octanol-water partition coefficient, vapor pressure, pKa, Henry’s Law Constant, and OH rate constant in the atmosphere. It started as a database of physical properties for chemicals being evaluated by SRC for the Hazardous Substances Data Bank (HSDB), available from the National Library of Medicine (NLM).

  • PIE TOOL | PATHWAY – SYSTEMS BIOLOGY – TEXT MINING
  • PIE (Protein Interaction information Extraction) the search is a configurable Web service to extract PPI-relevant articles from MEDLINE. By obtaining the PPI-related articles, biomedical researchers can easily find the up-to-date PPI information which cannot be found in manually curated PPI databases. Our goals in developing PIE are as follows: providing PPI-relevant articles from MEDLINE for biologists, providing baseline system performance for bio-text mining researchers, and providing a compact PubMed-search environment for PubMed users.

  • PINV (article) TOOL | NETWORKS – SYSTEMS BIOLOGY
  • The Protein Interaction Network Visualizer (PINV) is an open source, native web application that facilitates the visualization of protein interactions.

  • PK/DB DATABASE | ADME
  • PK/DB (a freely available database for pharmacokinetic properties) was designed with the aim of creating robust databases for pharmacokinetic studies and in silico ADME (Absorption, Distribution, Metabolism, and Excretion) prediction. The database contains high quality data for structurally diverse compounds associated with known ADME properties, including human oral bioavailability, human intestinal absorption, plasma protein binding, blood-brain barrier, among others.

  • PKKB (article) DATABASE | ADME – MOLECULAR DESCRIPTORS – PHARMACOKINETICS
  • The ADMET data currently in the PharmacoKinetics Knowledge Base (PKKB) are from 1685 drugs. All the FDA-approved smallmolecule drugs found in DrugBank have been collected into the PKKB.21 We categorize the data fields for each molecule into four groups: the general information, the pharmacological information, the physicochemical properties, and the ADMET properties (Table 1). The general information for each molecule includes the molecular name, synonyms, ACS number, and DrugBank ID. The pharmacological information for each molecule includes the status, the administration route, and the pharmacological effect. The physiochemical properties for each molecule include the experimental octanol/water partition coefficient (log P), the experimental aqueous solubility (log S), the experimental dissociation constant (pKa), the calculated octanol/water partition coefficient (log P), the calculated octanol/water distribution coefficient at pH = 7 (log D), the calculated aqueous solubility, the number of hydrogen bond donors, the number of hydrogen bond acceptors, the number of rotatable bonds, and the topological polar surface area (TPSA).

  • PLIO (article) THESAURI – TOOL | ONTOLOGY
  • The protein-ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand, and interaction, and was enriched by adding synonyms, useful annotations and references. The quality of the ontology was assessed based on structural, functional, and usability features. Validation of the lexicalized ontology by means of Natural Language Processing (NLP)-based methods showed a satisfactory performance (F-score=81%). Through integration into our information retrieval environment we can demonstrate that PLIO supports lexical search in PubMed abstracts. The usefulness of PLIO is demonstrated by two use case scenarios and it is shown that PLIO is able to capture both confirmatory and new knowledge from simulation and empirical studies.

  • PMT (article) PROJECT | PHARMACOLOGY
  • The Pharmacogenetics of Membrane Transporters (PMT) project was funded in 2000 and renewed in 2005. Their current research focuses on two major superfamilies, the Solute Carrier Superfamily (SLC) and the ATP Binding Cassette (ABC) Superfamily. Their SNP discovery studies include coding and non-coding regions of transporter genes. These studies focus on identifying genetic variants in membrane transporters in ethnically diverse populations. A fairly complete list of SLC and ABC transporters in the human genome is available. ThePharmacogenetics of Membrane Transporters (PMT) database provides information on genetic variants (including single nucleotide polymorphisms (SNPs) and insertions/deletions) in membrane transporter genes that have been discovered by the PMT project.

  • PPD (article) DATABASE | SYSTEMS BIOLOGY
  • The Plasma Proteome Database (PPD) was initially described in the year 2005 as a part of Human Proteome Organization’s (HUPO’s) pilot initiative on Human Plasma Proteome Project. Since then, improvements in proteomic technologies and increased throughput have led to identification of a large number of novel plasma proteins. To keep up with this increase in data, we have significantly enriched the proteomic information in PPD. This database currently contains information on 10 546 proteins detected in serum/plasma of which 3784 have been reported in two or more studies. The latest version of the database also incorporates mass spectrometry-derived data including experimentally verified proteotypic peptides used for multiple reaction monitoring assays. Other novel features include published plasma/serum concentrations for 1278 proteins along with a separate category of plasma-derived extracellular vesicle proteins. As plasma proteins have become a major thrust in the field of biomarkers, we have enabled a batch-based query designated Plasma Proteome Explorer, which will permit the users in screening a list of proteins or peptides against known plasma proteins to assess novelty of their data set.

  • PPI-Net PROJECT | NETWORK – SYSTEMS BIOLOGY
  • The Protein-Protein Interactions Network (PPI-Net) is a new National Network for Protein-Protein Interactions starting April 2011. The Network is jointly funded by Engineering and Physical Science Research Council (EPSRC), Biotechnology and Biological Sciences Research Council (BBSRC), and the Medical Research Council (MRC).

  • PRO THESAURI – TOOL | ONTOLOGY
  • PRO is a formal representation of protein objects, providing both descriptions of these objects and the relationships between them. PRO encompasses a sub-ontology of proteins based on evolutionary relatedness (ProEvo) and a sub-ontology of the multiple protein forms produced from a given gene (ProForm). PRO is interoperable with other OBO Foundry ontologies–such as the Sequence Ontology (SO) and the Gene Ontology (GO)–that provide representations of protein qualities. This interoperability facilitates cross-species comparisons, pathway analysis, disease modeling, and the generation of new hypotheses through data integration and machine reasoning.

  • ProbCMap (article)TOOL | NETWORK – SYSTEMS BIOLOGY MINING
  • Probabilistic drug connectivity mapping can be used to infer drug similarities based on drug treatment gene expression measurements from multiple cell lines, such as the Connectivity Map data. The Group Factor Analysis model is first applied to the expression data, separating cell line-specific responses from those that are shared by two or more cell lines. Drug similarities are then computed in the captured model space. In addition to single drug retrieval, also combinatorial retrieval is possible, searching for pairs of drugs that explain the query drug well.

  • Profilic (article) THESAURI – TOOL | ANNOTATION – PHARMACOLOGY – TEXT MINING
  • Prolific (protein-literature investigation for interacting compounds) provides a one-step solution to investigate available information on given protein names, sequences, similar proteins or sequences on the gene level. Co-occurrences of UniProtKB/Swiss-Prot proteins and PubChem compounds in all PubMed abstracts are retrievable. Concise ‘heat-maps’ and tables display frequencies of co-occurrences. They provide links to processed literature with highlighted found protein and compound synonyms. Evaluation with manually curated drug–protein relationships showed that up to 69% could be discovered by automatic text-processing.

  • PROMISCUOUS DATABASE | ADVERSE EVENT – PHARMACOLOGY – SYSTEMS BIOLOGY
  • PROMISCUOUS is an exhaustive resource of protein-protein and drug-protein interactions with the aim of providing a uniform data set for drug repositioning and further analysis. It contains three different types of entities: drugs, proteins and side-effects as well as relations between them. This resource delivers complex relations among drugs, their respective targets and side-effects of the drugs are presented in a user-friendly interface developed. For each entity detailed information is given. To enable the user to explore and handle the data in a scientific yet intuitive way, a novel interface that offers a “natural” way of exploring the network. Here database entities (drugs, targets and side effects) are represented as nodes in a network with edges, which represent the relations between them.

  • Protégé THESAURI – TOOL | ONTOLOGY
  • Protégé is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protégé implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protégé can be customized to provide domain-friendly support for creating knowledge models and entering data. Further, Protégé can be extended by way of a plug-in architecture and a Java-based Application Programming Interface (API) for building knowledge-based tools and applications.

  • PROTECTPROJECT | ADVERSE EVENT
  • The goal of PROTECT is to strengthen the monitoring of the benefit-risk of medicines in Europe. This will be achieved by developing a set of innovative tools and methods that will enhance the early detection and assessment of adverse drug reactions from different data sources, and enable the integration and presentation of data on benefits and risks. These methods will be tested in real-life situations in order to provide all stakeholders (patients, prescribers, public health authorities, regulators and pharmaceutical companies) with accurate and useful information supporting risk management and continuous benefit-risk assessment.

  • ProTox (article) TOOL | RISK ASSESSMENT – TOXENDPOINT
  • PROTOX is a webserver for the prediction of oral toxicities of small molecules in rodents. The prediction of compound toxicities is an important part of the drug design development process. Computational toxicity estimations are not only faster than the determination of toxic doses in animals, but can also help to reduce the amount of animal experiments. To read more about reducing animal testing, go to Animal Research For Life.

  • PubChem DATABASE | PHARMACOLOGY
  • PubChem provides information on the biological activities of small molecules. It is a component of NIH’s Molecular Libraries Roadmap Initiative. PubChem includes substance information, compound structures, and BioActivity data in three primary databases, Pcsubstance, Pccompound, and PCBioAssay, respectively.

  • PubChem Promiscuity (article) DATABASE – TOOL | DATA MINING – PHARMACOLOGY
  • PubChem Promiscuity counts allow for a better understanding of a compound’s assay activity profile and drug potential. Although PubChem contains a vast amount of compound and assay data, it currently does not have a convenient or efficient method to obtain in-depth promiscuity counts for compounds. PubChem promiscuity fills this gap. It is a Java servlet that uses NCBI Entrez (eUtils) web services to interact with PubChem and provide promiscuity counts in a variety of categories along with compound descriptors, including PAINS-based functional group detection.

  • PubChemDB (article) DATABASE – TOOL | DATA MINING – PHARMACOLOGY
  • PubChemDB is a Java API for working with PubChem data-sets. Features include: exposes most of the PubChem Schema as an object orientated API. To the authors knowledge this is the only public API for working with this schema; lets to download and assembly of PubChem data via NCBI web services and FTP; uses the Hibernate persistence framework – database agnostic and built in query/search; and integrates chemical structure search via JChem from Chemaxon; and Integrated curve fitting (derived from NCGC CurveFit).

  • PubTator THESAURI – TOOL | ANNOTATION – TEXT MINING
  • PubTator is a Web-based tool that allows curators to create, save, and export annotations. As shown in our past study manual curation can greatly benefit from (semi-)automated computer analysis. Hence, PubTator is equipped with multiple advanced computer algorithms for assisting two specific curation tasks: a) document triage and b) bioconcept annotation (e.g. genes).
    PubTator is developed based on a prototype system that was previously used at the NCBI for various manual curation projects such as annotating disease mentions in PubMed abstracts. In response to call for participation in BioCreative 2012, we significantly extended our previous system in developing PubTator. First, relevance ranking and concept highlighting were added to ease the task of document triage. Second, state-of-the-art named entity recognition tools (e.g. winning gene normalization systems in BioCreative III) were integrated to pre-tag bioconcepts of interest, as a way to facilitate the task of gene/disease/chemical annotation. Third, PubTator was developed to have a look-and-feel similar to PubMed, thus minimizing the learning efforts required for new users. Furthermore, a standard PubMed search option is made available in PubTator, which would allow our users to make a hassle-free move of their saved PubMed queries (a common practice for curators doing document triage) into this new curation system. Finally, by taking advantage of pre-tagging bioconcepts, PubTator also allows its users to do semantic search besides the traditional keyword based search, a novel feature not available in PubMed.

  • QSAR World DATABASE | QSAR MODELING
  • QSAR World is a free online resource dedicated to Quantitative Structure Activity Relationship (QSAR) modeling. It is an effort to build a vibrant and interactive community of QSAR professionals, researchers and students. They offer the latest and authentic data manually curated datasets compiled from several peer-reviewed journals in the domain of QSAR modeling.
    See their section Web-based Resources (free databases, free datasets and free programs links).

  • QSPR-THESAURUS DATABASE – PROJECT | QSAR MODELING
  • QSPR-THESAURUS has been developed within the EU FP7 CADASTER project. It contains physico-chemical data and models for four classes of compounds: Polybrominated diphenylethers (PBDE), Perfluoroalkylated substances, Substituted musks/fragrances and Triazoles/benzotriazoles.

  • Rat Genome Database (article) DATABASE – GENOMICS – SYSTEMS BIOLOGY
  • The Rat Genome Database (RGD) provides critical datasets and software tools to a diverse community of rat and non-rat researchers worldwide. To meet the needs of the many users whose research is disease oriented, RGD has created a series of Disease Portals and has prioritized its curation efforts on the datasets important to understanding the mechanisms of various diseases. Gene-disease relationships for three species, rat, human and mouse, are annotated to capture biomarkers, genetic associations, molecular mechanisms and therapeutic targets.

  • REACH REGULATORY GUIDELINES
  • The Registration, Evaluation, Authorisation and Restriction of Chemical substances (REACH) is an European Community Regulation on chemicals and their safe use (EC 1907/2006). The new law entered into force on 1 June 2007. The aim of REACH is to improve the protection of human health and the environment through the better and earlier identification of the intrinsic properties of chemical substances. The REACH Regulation gives greater responsibility to industry to manage the risks from chemicals and to provide safety information on the substances. Manufacturers and importers will be required to gather information on the properties of their chemical substances, which will allow their safe handling, and to register the information in a central database run by the European Chemicals Agency (ECHA) in Helsinki. The Agency will act as the central point in the REACH system: it will manage the databases necessary to operate the system, co-ordinate the in-depth evaluation of suspicious chemicals and run a public database in which consumers and professionals can find hazard information.

  • Renal Gene Expression Database (article) DATABASE | TOXENDPOINT – SYSTEMS BIOLOGY
  • The Renal Gene Expression Database (RGED)is a relational database of gene expression profiles in kidney disease.

  • RepDose DATABASE | TOXENDPOINT
  • RepDose (repeated dose toxicity) is a relational database on subacute to chronic toxicity and currently contains 655 chemicals. The toxicity of these chemicals is documented in about 2280 studies, carried out in rats, mice or dogs with oral or inhalation exposure. The database has been developed by Fraunhofer ITEM (Bitsch et al. 2006) with funding from Cefic LRI and grows continuously. Publicly available, predominantly peer-reviewed studies are entered in the RepDose database. Sources for data entry are e.g.: German MAK-Documentations, EHC, EU RAR, Reports from German BG Chemie, HPV-chemicals, NTP reports…

  • RePORT PROJECT – TOOL
  • The Research Portfolio Online Reporting Tools (RePORT) Website provides a central point of access to reports, data, and analyses of NIH research.

  • REPROTOX® (commercial) DATABASE | DRUG SAFETY – RISK ASSESSMENT – TOXENDPOINT
  • REPROTOX® is an information system developed by the Reproductive Toxicology Center for its members. REPROTOX contains summaries on the effects of medications, chemicals, infections, and physical agents on pregnancy, reproduction, and development. The REPROTOX® system was developed as an adjunct information source for clinicians, scientists, and government agencies. Patients should consult their health care providers rather than relying on REPROTOX® summaries.

  • RICORDO DATABASE – PROJECT – TOOL
  • The RICORDO project is focused on the study and design of a multiscale ontological framework in support of the Virtual Physiological Human community to improve the interoperability amongst its Data and Modelling resources. To this end, it aims to build directly upon the shared experiences and published recommendations emerging from the VPH Network of Excellence and ELIXIR initiatives.
    RICORDO draws together a number of key databases at the UK-based European Bioinformatics Institute (ArrayExpress, Reactome, BioModels, EnsEMBL, UniProt, ChEBI) along with tools, methods and significant input from different institutions.

  • RightField (article) THESAURI – TOOL | ONTOLOGY
  • RightField is an open source application that provides a mechanism for embedding ontology annotation support for Life Science data in Excel spreadsheets. Individual cells, columns or rows can be restricted to particular ranges of allowed classes or instances from chosen ontologies. The RightField-enabled spreadsheet presents selected ontology terms to the users as a simple drop-down list, enabling scientists to consistently annotate their data. The result is ‘semantic annotation by stealth’, with an annotation process that is less error-prone, more efficient, and more consistent with community standards.

  • RITA DATABASE – PROJECT | TOXENDPOINT
  • The purpose of the project RITA (Registry of Industrial Toxicology Animal-data) is to centralize the collection of historical data of control animals used on rodent carcinogenicity studies from different laboratories in a consistent manner. The availability of harmonised data from these studies in a comprehensive database can make the decisive difference in interpretation of these data. This tumor data base is a unique international cooperation between chemical and pharmaceutical companies and a non-profit organisation. It is maintained by the Fraunhofer Institute of Toxicology and Experimental Medicine (ITEM) Hannover. The cross organisational review of studies means that the histopathological assessment of tumors meets optimized standards for reliability, robustness and quality.
    RITA is much more than a data archive. The joint effort of the participants has created a communication platform for the conduct, evaluation and assessment of rodent carcinogenicity studies, including study design, technical procedures, diagnostic approaches, development of the database hardware platform, recognition by regulatory agencies and more. With these features RITA is facilitating the standardization for the conduct and histopathological evaluation of carcinogenicity studies. Such studies are requested by regulatory authorities in the course of the human risk assessment of chemicals or pharmaceuticals.

  • RS-WebPredictor (article) TOOL | CYP450 – METABOLISM – PHARMACOLOGY
  • Regioselectivity-WebPredictor (RS-WebPredictor) is a server that predicts isozyme-specific cytochrome P450 (CYP)-mediated sites of metabolism (SOMs) on drug-like molecules. Predictions may be made for the promiscuous 2C9, 2D6 and 3A4 CYP isozymes, as well as CYPs 1A2, 2A6, 2B6, 2C8, 2C19 and 2E1. RS-WebPredictor is the first freely accessible server that predicts the regioselectivity of the last six isozymes.

  • RTECS DATABASE | TEXT MINING – TOXENDPOINT
  • RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments.

  • SAFE-T PROJECT | BIOMARKER – TOXENPOINT
  • SAFE-T is working to address the current lack of sensitive and specific clinical tests to diagnose and monitor drug-induced injury to the kidney, liver and vascular systems in man, which is a major hurdle in drug development.

    Therefore, many promising candidate drugs with pre-clinical kidney, liver or vascular toxicity signals of unknown relevance do not enter the clinical phase, as no sensitive tests exist to allow timely detection of patient safety signs before irreversible injury occurs. New tests based on biomarkers will enable studies to assess whether these drugs are safe to ‘translate’ into clinical use. Furthermore, the new translational safety biomarkers will allow the identification and management of side effects of drugs throughout drug development helping to reduce the risk of developing medicines and improving the safety management of patients.
    SAFE-T work generally falls under the goal of creating methods to enable personalised medicines that improve public health.

  • SafeSciMET PROJECT | DRUG SAFETY
  • SafeSciMET has established a pan-European education and training network, which solves a shortfall identified by EUFEPS in current drug safety education and training in Europe where an integrative and translational approach is lacking. The public consortium consists of top academic institutions for drug safety education and research and Industrial pharmaceutical companies, all members of EFPIA.
    The SafeSciMET together with the coordinators of other IMI E&T topics, will participate in the Strategic Coordination Board to ensure coordination between the IMI E&T topics.

  • Safety Intelligence Program PROJECT | DRUG SAFETY – RISK ASSESSMENT
  • The Safety Intelligence Program from BioWisdom is an industry-sponsored initiative that embraces the expertise of its pharmaceutical members and other stakeholders to build the world’s most comprehensive intelligence resource for use in improving drug safety assessments. Joining the program brings a wealth of benefits, including access to the Safety Intelligence System and participation in an interactive community under the Safety Intelligence Program Members Forum.

  • SBKB DATABASE | PHARMACOLOGY
  • The Structural Biology Knowledgebase (SBKB) is a free, comprehensive resource produced in a collaboration between the Protein Structure Initiative (PSI) and Nature Publishing Group (NPG). The site offers you an easy way of keeping abreast of developments both by the PSI and more generally in the fields of structural genomics and structural biology. The SBKB serves as a continually updated portal to research data and other resources from the PSI. NPG provides a monthly update with synopses of important research advances, recent additions to a categorized library of research articles, as well as news and events in structural biology. One can register to receive a monthly email newsletter and subscribe to own RSS feeds.

  • Scaffold Hunter (article) TOOL | PHARMACOLOGY
  • Scaffold Hunter is a JAVA-based software tool for the analysis of structure-related biochemical data. It facilitates the interactive exploration of chemical space by enabling generation of and navigation in a scaffold tree hierarchy annotated with various data. The graphical visualization of structural relationships allows to analyze large data sets, e.g., to correlate chemical structure and biochemical activity.

  • Scaffold network generator (article) TOOL | PHARMACOLOGY
  • Scaffold network generator (SNG) is an open-source command-line utility that computes the hierarchical network of scaffolds that define a large set of input molecules, a tool for mining molecular structures.

  • sc-PDB DATABASE | MOLECULAR DESCRIPTORS – PHARMACOLOGY
  • The sc-PDB database is an annotated archive of druggable binding sites extracted from the Protein Data Bank. It contains all-atoms coordinates for 8166 protein–ligand complexes, chosen for their geometrical and physico-chemical properties. The sc-PDB provides a functional annotation for proteins, a chemical description for ligands and the detailed intermolecular interactions for complexes. The sc-PDB now includes a hierarchical classification of all the binding sites within a functional class. The current release 2010.2 on line contains: 8166 entries, 2636 proteins and 4229 ligands.

  • SciFinderTOOL | TEXT MINING
  • The SciFinder is a research discovery tool that allows college students and faculty to access a wide diversity of research from many scientific disciplines, including biomedical sciences, chemistry, engineering, materials science, agricultural science.

  • ScrumPy TOOL | METABOLISM
  • ScrumPy is an open-source (GPL) Python tool kit for metabolic modelling of Cell Systems Modelling Group (http://mudshark.brookes.ac.uk/index.php/Home), being used and developed by CSMG. It currently provides kinetic and sturctural modelling facilities, including steady-state determination, time-course simulation, MCA functions, determination of Elementary Modes and enzyme subsets.

  • Semantator (article) TOOL | ANNOTATION – IDENTIFIER -TEXT MINING
  • Semantator (Semantic Annotator), a semantic-web-based environment for annotating data of interest in biomedical documents, browsing and querying the annotated data, and interactively refining annotation results if needed. Through Semantator, information of interest can be either annotated manually or semi-automatically using plug-in information extraction tools. The annotated results will be stored in RDF and can be queried using the SPARQL query language. In addition, semantic reasoners can be directly applied to the annotated data for consistency checking and knowledge inference.

  • Semantic Measures Library (article) TOOL | ANNOTATION – TEXT MINING
  • The Semantic Measures Library (SML) is a tool dedicated to the computation, development and analysis of semantic measures; an open source resource that supports various ontology formats and specifications.

  • SemMedDB (article) DATABASE – TOOL | TEXT MINING
  • Semantic MEDLINE Database (SemMedDB) is a repository of semantic predications (subject-predicate-object triples) extracted by SemRep, a semantic interpreter of biomedical text. SemMedDB currently contains information about approximately 57.6 million predications from all of PubMed citations (more than 21 million citations, as of June 30th, 2012) and forms the backbone of Semantic MEDLINE application.

  • SEND Explorer TOOL | REGULATORY GUIDELINES
  • SEND Explorer is a web-based viewer for use with SEND (Standard for Exchange of Nonclinical Data) datasets. SEND Explorer merges study and subject metadata with results data to make it easy to review, QC, and query your SEND data. SEND Explorer displays results in a grid by domain. Columns can be hidden and shown, and data can be filtered and sorted to create meaningful displays which can be exported to CSV for further analysis using third-party tools such as Excel or Spotfire.

  • SESL PROJECT
  • The Pistoia Alliance was first conceived by informatics experts at AstraZeneca, GSK, Novartis, and Pfizer who were together attending a meeting in Pistoia, Italy. During the meeting and ensuing conversations, Pistoia’s founders realized that their organizations were all individually tackling the same precompetitive problems—issues around aggregating, accessing, and sharing data that are essential to innovation, but provide little competitive advantage. They realized that working together to solve these common problems would free their organizations to innovate by enabling them to cut costs and repurpose precious resources to projects with more strategic, competitive impact.
    The Pistoia Alliance was established as a members’ organization in 2009. Today, it encompasses ife science companies, academic groups, informatics vendors, and publishers. Together, Pistoia Alliance members aim to lower barriers to innovation by improving the interoperability of R&D business processes through precompetitive collaboration. The organization focuses on bringing stakeholders to the table to define common, conceptual steps of the life science R&D workflow.

  • SEURAT-1 PROJECT | RISK ASSESSMENT – TOXENDPOINT
  • SEURAT was presented by the FP7 HEALTH Theme in 2008 as the long-term target in safety testing. The Research Initiative launched by the European Commission and Cosmetics Europe (“Towards the replacement of in vivo repeated dose systemic toxicity testing”) is called “SEURAT-1”, indicating that this is a first step in a specific area addressing the global long-term strategic target SEURAT. The “Safety Evaluation Ultimately Replacing Animal Testing”(SEURAT) vision is to fundamentally change the way we assess the safety of chemicals, by superseding traditional animal experiments with a predictive toxicology that is based on a comprehensive understanding of how chemicals can cause adverse effects in humans.

  • Sharing Clinical Research Data Workshop Summary OTHER
  • Sharing Clinical Research Data Workshop Summary, October 2012, organized by the Institute of Medicine (US), identifies barriers and challenges to sharing clinical research data, explores strategies to address these barriers and challenges, including identifying priority actions and “low-hanging fruit” opportunities, and discusses strategies for using these potentially large datasets to facilitate scientific and public health advances.

  • SIDER DATABASE | ADVERSE EVENT – PHARMACOLOGY
  • SIDER contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations.

  • SKOS THESAURI – TOOL
  • The Simple Knowledge Organization System (SKOS) is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading systems and taxonomies within the framework of the Semantic Web. Use these two converters: OWLtoSKOS and OBOtoSKOS.

  • SMARTCyp (article) TOOL | CYP450 – METABOLISM
  • SMARTCyp predicts the sites in molecules that are most liable to cytochrome P450 mediated metabolism.

  • SMPDB DATABASE | METABOLISM – PATHWAY – SYSTEMS BIOLOGY
  • SMPDB (The Small Molecule Pathway Database) is an interactive, visual database containing more than 350 small molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.

  • SPARC TOOL | MOLECULAR DESCRIPTORS
  • SPARC is a web application to calculate pKa, Gas pKa, NonAq pKa, Solid pKa, log D and other properties.

  • STITCH DATABASE | PHARMACOLOGY
  • The Search Tool for Interactions of Chemicals (STITCH) is a knowledge database to explore known and predicted interactions between proteins and small-molecule chemicals for understanding of molecular and cellular functions. Over 68,000 chemicals are represented. STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. STITCH contains interactions for over 74,000 small molecules and over 2.5 million proteins in 630 organisms.

  • SOMEViz (article) TOOL | CYP450 – METABOLISM
  • SOMEViz (Site of Metabolism Estimator Visualization) is an open-accessed web server for rapidly exploring potential SOM (Sites of Metabolism) of small molecules. It provides prediction of human cytochromes p450 (CYP450)-mediated biotransformations for the six most important metabolic reactions.

  • SOMP (article) TOOL | CYP450 – METABOLISM – PHARMACOLOGY – STRUCTURE-BASED PREDICTION
  • SOMP is a new freely available web server site of metabolism predictor to predict the sites of metabolism (SOM) based on the structural formula of chemicals has been developed. It is based on the analyses of ‘structure-SOM’ relationships using a Bayesian approach and labelled multilevel neighbourhoods of atoms descriptors to represent the structures of over 1000 metabolized xenobiotics. The server allows predicting SOMs that are catalysed by 1A2, 2C9, 2C19, 2D6 and 3A4 isoforms of cytochrome P450 and enzymes of the UDP-glucuronosyltransferase family.

  • Strategies for Sharing Clinical Trial Data PROJECT
  • An ad hoc committee of the Institute of Medicine will conduct a study to develop guiding principles and a framework (activities and strategies) for the responsible sharing of clinical trial data. For the purposes of the study, the scope will be limited to interventional clinical trials and “data sharing” will include the responsible entity (data generator) making the data available via open or restricted* access, or exchanged among parties. For the purposes of this study, data generator will include industry sponsors, data repositories, and researchers conducting clinical trials.

  • SuperCYP DATABASE | CYP450 – METABOLISM – PHARMACOLOGY
  • This is a database devoted to CYP450 that contains about 1,170 drugs, 2,785 Cytochrome-Drug interactions and about 1,200 alleles.

  • SuperDrug DATABASE – THESAURI| IDENTIFIER – PHARMACOLOGY
  • The SuperDrug database contains ∼2500 3D-structures of active ingredients of essential marketed drugs. To account for structural flexibility they are represented by 105 structural conformers. Here we present a web-query system enabling searches for drug name, synonyms, trade name, trivial name, formula, CAS-number, ATC-code etc. 2D-similarity screening (Tanimoto coefficients) and an automatic 3D-superposition procedure based on conformational representation are implemented. Drug structures above a similarity threshold as well as superimposed conformers can be retrieved in the mol- file format via a graphical interface.

  • SuperPred (article) TOOL | PHARMACOLOGY – STRUCTURE-BASED PREDICTION – SYSTEMS BIOLOGY
  • The SuperPred is a prediction webserver for ATC code and target prediction of compounds. Predicting ATC codes or targets of small molecules and thus gaining information about the compounds offers assistance in the drug development process. The webserver’s ATC predicition as well as target prediction is based on a pipeline consisting of 2D, fragment and 3D similarity search. The drug classification for a compound can be performed at the Drug Classification site. Target prediction for an input compound can be executed at the Target-Prediction site.

  • SuperTarget DATABASE – THESAURI | DRUG SAFETY – METABOLISM – ONTOLOGY – PATHWAY
  • SuperTarget integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins.

  • SuperToxic (article) DATABASE – THESAURI | RISK ASSESSMENT – TOXENDPOINT
  • SuperToxic is a database that collects toxic compounds from literature and web sources.The current version of this database compiles approx. 60,000 compounds with about 100,000 synonyms. These molecules are classified according to their toxicity based on more than 2,500,000 measurements. The commercial availability is documented for about 5,000 toxic compounds.The SuperToxic database provides a variety of search options like name, CAS number, molecular weight or measured values of toxicity.The collection of this data together with the functionality enables the evaluation of the risks of newly designed compounds and indication of biological interactions with the aid of similarity searches. Furthermore, a connection to the KEGG database is available to allow the identification of those pathways the searched compounds are involved in.

  • SureChem DATABASE – THESAURI | PHARMACOLOGY – WORKFLOW
  • SureChem offers the only in-house database of chemical structures and names extracted from the full text collections of US, EP and WO patents. This unmatched patent chemistry collection can be easily added to any customer workflow or analysis tools, completely behind the firewall. Perform virtual screens of proprietary compounds before starting exhaustive IP searches. Run internal compound libraries against the total patent chemistry landscape.
    Updated chemical structures are extracted and delivered to customers within 24 hours of patent and application publication. The SureChem Database is easily loaded into all database software (Oracle, DB2, MySQL etc). Query results from the in-house database can be linked to SureChem Portal so users can view structures within the context of the patent document.
    From December 2013 this database becomes part of ChEMBL database.

  • SureChEMBL DATABASE | PHARMACOLOGY
  • SureChEMBL is a live system, which is continuously extracting chemical entities (in text, images and attached mol files) from patent documents provided by the main patent authorities (WIPO, EPO and USPTO). SureChEMBL facilitates the search of the patent literature using Lucene-based keyword queries and, much more importantly, chemistry-based queries.
    Currently, it contains 15,773,144 unique compounds and 12,961,024 annotated patents. Approximately 80,000 new compounds extracted from 50,000 new patents are added to the system monthly. Moreover, the latency for a new patent document from its application date to becoming searchable in the system ranges between 2 and 7 days, in most cases.

  • SurvExpress (article) DATABASE | BIOMARKER – SYSTEMS BIOLOGY
  • SurvExpress is a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. They generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues, and implemented it as a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. The utility and simplicity of SurvExpress is exemplified by two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis.

  • Swissprot DATABASE | PHARMAOCOLOGY
  • The UniProt Knowledgebase consists of: UniProtKB/Swiss-Prot; a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases [More details / References / Linking to UniProtKB/Swiss-Prot / User manual / Recent changes / Disclaimer], and UniProtKB/TrEMBL; a computer-annotated supplement of Swiss-Prot that contains all the translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot.

  • T3DB DATABASE – THESAURI| RISK ASSESSMENT
  • Toxin and Toxin Target Database (T3DB) is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. The database currently houses over 2900 toxins described by over 34 200 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to over 1300 corresponding toxin target records. Altogether there are over 33 800 toxin, toxin target associations. Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5600 sources, which include other databases, government documents, books, and scientific literature. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches.

  • Target Dossier TOOL | TEXT MINING
  • The Target Dossier GUI (TDGUI) is an application whose main goal is the integration of drug target’s data to identify the most productive points for therapeutic intervention. It is been developed within the context of the IMI project OpenPHACTS and relies on the knowledge discovery platform and APIs developed by the consortium.The application is in stable version 1.0 but still in development as many features can and will be added shortly.

  • Target Protein Database (article) DATABASE | METABOLISM – PHARMACOLOGY
  • The Reactive Metabolite Target Protein Database (TPDB) is a comprehensive, curated, searchable, documented compilation of publicly available information on the protein targets of reactive metabolites of 18 well-studied chemicals and drugs of known toxicity. TPDB software enables i) string searches for author names and proteins names/synonyms, ii) more complex searches by selecting chemical compound, animal species, target tissue and protein names/synonyms from pull-down menus, and iii) commonality searches over multiple chemicals. Tabulated search results provide information, references and links to other databases.

  • TarPred (article) TOOL | PHARMACOLOGY – STRUCTURE-BASED PREDICTION
  • TarPred is an online implementation of a recently published computational model for target prediction, based on a reference library containing 533 individual targets with 179 807 active ligands. TarPred accepts interactive graphical input or input in the chemical file format of SMILES. Given a query compound structure, it provides the top ranked 30 interacting targets.

  • The NCBI Taxonomy Homepage THESAURI
  • TETRATOX DATABASE | TOXENDPOINT
  • The TETRATOX database is a collection of toxic potency data for more than 2,400 industrial organic compounds of which more than 1,600 have been published. The assay {Schultz, T.W. 1997. TETRATOX: Tetrahymena pyriformis population growth impairment endpoint-A surrogate for fish lethality. Toxicol. Methods 7: 289-309}is a short-term, static protocol using the common freshwater ciliate Tetrahymena pyriformis (strain GL-C). The 50% impairment growth concentration (IGC50) is the recorded endpoint.
    The NCBI Taxonomy Homepage offers direct links to some of the organims commonly used in molecular research projects.

  • TIMES TOOL | METABOLISM – TOXENDPOINT
  • The TIssue MEtabolism Simulator (TIMES) is a heuristic algorithm to generate plausible metabolic maps from a comprehensive library of biotransformations and abiotic reactions. It allows prioritization of chemicals according to toxicity of their metabolites. The list of transformations is prioritized based on estimated system-specific probabilities of occurrence of these transformations.The ability of TIMES to predict on same platform the metabolism of chemicals and toxicity resulting from their metabolic activation is an important advantage of the method. Presently, TIMES platform is used to predict the following metabolism activated endpoints: Skin sensitization, AMES Mutagenicity, Chromosomal aberration and Receptor mediated endpoints.

  • TISGED DATABASE | GENOMICS
  • The Tissue-Specific Genes Database (TISGED) is a free database that provides comprehensive information of tissue-specific genes derived from biomedical literatures and data mining of more than 123,125 gene expression profiles over 107 human tissues, 67 mouse tissues and 30 rat tissues. A statistical parameter, SPM, is introduced to quantitatively measure the relative specificity of a gene over tissues.

  • Toolbox v3.3 TOOL | QSAR MODELING – STRUCTURE-BASED PREDICTION
  • The Toolbox is a software application intended to be used by governments, chemical industry and other stakeholders in filling gaps in (eco)toxicity data needed for assessing the hazards of chemicals. The Toolbox incorporates information and tools from various sources into a logical workflow.

  • ToxAlerts (article) DATABASE – TOOL | RISK ASSESSMENT – STRUCTURE-BASED PREDICTION
  • ToxAlerts is a Web-based platform for collecting and storing toxicological structural alerts from literature and for virtual screening of chemical libraries to flag potentially toxic chemicals and compounds that can cause adverse side effects. the platform can be easily used for fast virtual screening of large chemical datasets, focused libraries, or newly designed compounds against the toxicological alerts, providing a detailed profile of the chemicals grouped by structural alerts and endpoints. Such a facility can be used for decision making regarding whether a compound should be tested experimentally, validated with available QSAR models, or eliminated from consideration altogether. The alert-based screening can also be helpful for an easier interpretation of more complex QSAR models. The system is publicly accessible and tightly integrated with the Online Chemical Modeling Environment (OCHEM, http://ochem.eu). The system is open and expandable: any registered OCHEM user can introduce new alerts, browse, edit alerts introduced by other users, and virtually screen his/her data sets against all or selected alerts. The user sets being passed through the structural alerts can be used at OCHEM for other typical tasks: exporting in a wide variety of formats, development of QSAR models, additional filtering by other criteria, etc. The database already contains almost 600 structural alerts for such endpoints as mutagenicity, carcinogenicity, skin sensitization, compounds that undergo metabolic activation, and compounds that form reactive metabolites and, thus, can cause adverse reactions. The ToxAlerts platform is accessible on the Web at http://ochem.eu/alerts, and it is constantly growing.

  • ToxBank (article) DATABASE | RISK ASSESSMENT – TOXENDPOINT
  • ToxBank establishes a dedicated web-based warehouse for toxicity data management and modelling, a “gold standards” compound database and repository of selected test compounds, and a reference resource for cells, cell lines and tissues of relevance for in vitro systemic toxicity research carried out across the FP7 HEALTH.2010.4.2.9 Alternative Testing Strategies SEURAT program. The project develops infrastructure and service functions to create a sustainable predictive toxicology support resource going beyond the lifetime of the program.

  • ToxCast™ Program (article) TOOL | RISK ASSESSMENT – TOXENDPOINT
  • In 2007, EPA launched ToxCast™ to develop a cost-effective approach for efficiently prioritizing the toxicity testing of thousands of chemicals.

  • ToxHunter DATABASE | METABOLISM – PHARMACOLOGY – RISK ASSESSMENT
  • ToxHunter is a systems toxicology knowledgebase and data analysis package designed for the assessment of safety liabilities of drugs, environmental contaminants and other xenobiotics at all stages of discovery and development. ToxHunter is available as an add-on for GeneGo MetaCore and MetaDrug systems biology and systems pharmacology solutions, and integrates seamlessly with these products.

  • Toxicological Abbreviations THESAURI
  • List of abbreviations related to toxicology gathered on May of 1998.

  • ToxML (article) THESAURI | TOXENDPOINT
  • The Toxml is an XML standard database based on toxicity controlled vocabulary for use in database standardization. The ToxML language along with databases will be developed in the following areas: genetic toxicity, carcinogenicity, chronic toxicity, sub-chronic toxicity, reproductive and developmental toxicity, clinical effects, skin sensitization, environmental fate and toxicity.

  • TOXNET DATABASE | RISK ASSESSMENT – TOXENDPOINTS
  • The TOXNET is a compendium of databases on toxicology, hazardous chemicals, environmental health, and toxic releases.

  • ToxPi DATABASE – TOOL | MOLECULAR DESCRIPTORS – RISK ASSESSMENT – TOXENDPOINTS
  • ToxPi GUI (Toxicological Priority Index graphical user interface) is a flexible prioritization support software tool based on the “Endocrine Profiling and Prioritization of Environmental Chemicals Using ToxCast Data” article by David M. Reif et al. that incorporates chemical’s bioactivity profiles, inferred toxicity pathways, dose estimates, exposure data, chemical structural descriptors, etc.

  • ToxPredict TOOL | RISK ASSESSMENT – TOXENDPOINTS
  • ToxPredict is a Graphical User Interface (GUI) for predicting toxicity developed in the framework of OpenTox project.

  • ToxRefDB Program DATABASE | TOXENDPOINT
  • The Toxicity Reference Database (ToxRefDB) was developed by the National Center for Computational Toxicology (NCCT) in partnership with EPA’s Office of Pesticide Programs (OPP), to store data from in vivo animal toxicity studies. The initial focus was populating ToxRefDB with pesticide registration toxicity data that has been historically stored as hard-copy and scanned documents by OPP. A significant portion of these data have now been processed into ToxRefDB in a standardized and structured format. ToxRefDB currently includes chronic, cancer, sub-chronic, developmental, and reproductive studies on hundreds of chemicals, many of which are pesticide active ingredients. These data are now accessible and computable within ToxRefDB, and are serving as reference toxicity data for ORD research and OPP retrospective analyses. The primary research appliction of ToxRefDB is to provide toxicity endpoints for the development of ToxCast™ predictive signatures.

  • Toxtree TOOL | RISK ASSESSMENT – TOXENDPOINT
  • The Toxtree is a flexible and user-friendly open-source application that places chemicals into categories and predicts various kinds of toxic effect by applying decision tree approaches.

  • ToxWiz DATABASE – TOOL | QSAR MODELING – TOXENDPOINT
  • ToxWiz is a software solution for predicting toxic endpoints and for elucidating mechanisms of toxicity. It allows you to understand on- and off- target mechanisms of action of your compounds, thus minimizing the number of animal testing wherever possible. It helps prioritize new experiments and speeds up the overall decision making process. It uses novel algorithms to predict toxic end-points. This approach to predictive toxicology offers a new perspective in this field, being highly complementary to well-established QSAR and other approaches.

  • Toxygates (article) DATABASE | GENOMICS – TOXENDPOINT
  • Toxygates is a user-friendly integrated analysis platform for the Japanese Toxicogenomics Project (TGP) database that combines a large microarray dataset with the ability to fetch semantic linked data, such as pathways, compound-protein interactions and orthologs, on demand. It can also perform pattern-based compound ranking with respect to the expression values of a set of relevant candidate genes. By using Toxygates, users can freely interrogate the transcriptome’s response to particular compounds and conditions, which enables deep exploration of toxicity mechanisms.

  • TP-search (article) DATABASE | PHARMACOKINETICS – PHARMACOLOGY
  • The Transporter database, TP-search, is a comprehensive database on drug transporters, which are thought to play an important role in pharmacokinetics of drugs. All the information is extracted from a large number of published papers. With this database, users can obtain various kinds of basic information on drug transporters.

  • TrialTrove DATABASE | DRUG SAFETY
  • TrialTrove delivers the world’s most comprehensive ongoing clinical trials information, tracking up to three times as many trials as the next most popular data source. It is a single, integrated intelligence solution that saves dramatic amounts of research time and delivers exceptional return on investment, covering interventional drug trials from Phase I to Phase IV. TrialTrove provides the deepest and most detailed intelligence in addition to giving a complete picture of competitors’ clinical programs by therapeutic area and disease, by analysing and investigating what’s going on behind the raw information.

  • UGT Alleles Nomenclature THESAURI | METABOLISM – PHARMACOLOGY
  • This website is devoted to recommended nomenclature for the human polymorphic UGT genes, only humand UGT alleles are considered. Scientists worldwide are encouraged to use this nomenclature guidelines to avoid “home-made” allelic designations that can confuse the nomenclature system and the scientific literature.

  • UM-BBD DATABASE | METABOLISM – PATHWAY
  • The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.
    The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes.

  • UMLS THESAURI
  • The UMLS, or Unified Medical Language System, is a set of files and software that brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems.

  • UPdb (article) DATABASE | BIOMARKERS
  • The Urinary Proteome database contains data for fractionation methods (separation technique or chip-type, capillary electrophoresis elution time), mass analyzer used (general technique and specific MS instrumentation used), peak specific data (average m/z and intensity and frequency above threshold), study-centric information, experimental conditions (input volumes, wash conditions for solid phase extraction methods, andmatrix used), protein links (identified protein name, accession number and link to external databases and internal PADB crossreferences), and sample specific data (whether the sample was in vitro digested or not, from which tissue it originated, and whether it was further fractionated into subcellular components).

  • URSA (article) DATABASE | SYSTEMS BIOLOGY
  • Unveiling RNA Sample Annotation (URSA) leverages the complex tissue/cell-type relationships and simultaneously estimates the probabilities associated with hundreds of tissues/cell-types for any given gene expression profile. URSA provides accurate and intuitive probability values for expression profiles across independent studies and outperforms other methods, irrespective of data preprocessing techniques. Moreover, without re-training, URSA can be used to classify samples from diverse microarray platforms and even from next-generation sequencing technology.

  • VAERS DATABASE | ADVERSE EVENT – RISK ASSESSMENT
  • The Vaccine Adverse Event Reporting System (VAERS) is a national vaccine safety surveillance program co-sponsored by the Centers for Disease Control and Prevention (CDC) and the Food and Drug Administration (FDA). VAERS is a post-marketing safety surveillance program, collecting information about adverse events (possible side effects) that occur after the administration of vaccines licensed for use in the United States.

  • VEGA TOOL | QSAR MODELING
  • Using the VEGA platform, you can access a series of QSAR (quantitative structure-activity relationship) models for regulatory purposes, or develop your own model for research purposes. QSAR models can be used to predict the property of a chemical compound, using information obtained from its structure.

  • VigiBase™ (commercial) TOOL | ADVERSE EVENT – DRUG SAFETY – TEXT MINING
  • VigiBase™ is a unique collection of international drug safety data. The data is available in a wide range of services, from advanced neural network analysis to basic case report retrieval. The VigiBase™ services will help you find useful information about the safety profile of your products as well as your competitors’.
    The services are used by pharmaceutical companies to get data with global coverage and compare the ADR profile of their product with other products. Other common usage areas are: signal detection, updating PSURs (Product Safety Update Reports) and to compare with the reports in your own company database. The data held is collected from countries participating in WHO Programme for International Drug Monitoring. The member countries have access to the collected data and analyse it in
    order to investigate potential ADR signals and statistics and listings are also made on behalf of pharmaceutical companies and academia.VigiBase™ comprises more than 3.8 million case reports, to which around 50,000 new reports are added quarterly. All of these cases are available to anyone with a health professional degree-level

    education (physician, dentist, nurse, pharmacist).

  • VirtualToxLab™ (commercial) (article), OpenVirtualToxLab™ (commercial) (article) TOOL | CYP450 – METABOLISM – PHARMACOLOGY – QSAR MODELING – STRUCTURE-BASED PREDICTION
  • The VirtualToxLab™ is an in silico tool for predicting the toxic potential (endocrine and metabolic disruptors, interference with ion channels) of drugs, chemicals and natural products by simulating and quantifying their interactions towards a series of proteins known to trigger adverse effects using
    automated, flexible docking combined with multi-dimensional QSAR (mQSAR). Currently, the VirtualToxLab comprises 16 validated models for the androgen, aryl hydrocarbon, estrogen α/β, hERG, glucocorticoid, liver X, mineralocorticoid thyroid α/β, and peroxisome proliferator-activated receptor γ as well as for the enzymes CYP450 1A2, 2A13, 2C9, 2D6 and 3A4. In contrast to other approaches in the field, the VirtualToxLab allows to rationalize a prediction at the molecular level by analyzing the binding mode. Access to the VirtualToxLab is available for all science-oriented organizations.
    The OpenVirtualToxLab™ is a forum for the calculation and exchange of in silico toxicity data. It has been launched for institutional users with occasional need of the technology and is freely available to non-profit organizations. The Biographics Laboratory 3R may publish selected results — binding modes and affinities, toxic potential — for compounds of general interest generated by a user of the OpenVirtualToxLab™ technology in scientific journals, its website or present at scientific conferences. The user will be informed beforehand and he/she may request postponing the publication/presentation or, given good reasons, veto it.

  • Vitic (commercial) DATABASE | QSAR MODELING – RISK ASSESSMENT – STRUCTURE-BASED PREDICTION – TOXENDPOINT
  • Vitic is a toxicity database that has been specially developed for researchers who need efficient access to toxicology information, even when the information resides in multiple databases in different locations. Vitic is a chemically intelligent database, which can recognise and search for similarities in chemical
    structures. This makes it an essential research tool for Toxicologists working in Drug Discovery or Product Safety, and Vitic is especially useful in (Quantitative) Structure-Activity Relationship (QSAR) modelling.

  • Voronto (article) THESAURI – TOOL
  • Voronto is a tool that integrates expression data and biological ontologies, allowing the analyst to explore the whole ontology and detect changes on expression patterns inside the ontology.

  • WDI index THESAURI | IDENTIFIER – PHARMACOLOGY
  • The World Drug Index is an authoritative index for marketed and development drugs. With internationally-recognized drug names, synonyms, trade names, trivial names and trial preparation codes in one source, plus compound structures and activity data, it is ideal for finding instant answers to

    drug research and marketing queries.

  • WebChem Viewer (article) DATABASE – TOOL
  • Sharing lists of molecular structures with associated chemical properties is a common task in computer-aided drug design and medicinal chemistry. WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed in any modern web browser, on any operating system (including mobile), without requiring the installation of additional software. The output can also be easily incorporated into existing web page.

  • WebProtegé (article) THESAURI – TOOL | ONTOLOGY
  • WebProtégé is an open source, lightweight, web-based ontology editor. WebProtégé provides a friendly and highly configurable user interface that can be adapted for the use of domain experts. It has support for form-based editing and full-fledged collaboration. Documentation available.

  • WhichCyp TOOL | METABOLISM
  • WhichCyp, a tool for prediction of which cytochromes P450 isoforms (among 1A2, 2C9, 2C19, 2D6 and 3A4) a given molecule is likely to inhibit. The models are built from experimental high-throughput data using support vector machines and molecular signatures.

  • Wikigenes DATABASE | PHARMACOLOGY
  • WikiGenes is the first wiki system to combine the collaborative and largely altruistic possibilities of wikis with explicit authorship. In view of the extraordinary success of Wikipedia there remains no doubt about the potential of collaborative publishing, yet its adoption in science has been limited.

  • XenoSite (article) TOOL | CYP450 – ADME – METABOLISM
  • XenoSite Web provides prediction web services for small molecule biochemistry. XenoSite Web can be used by medicinal chemists and biologists to make predictions about the human in vivo metabolism of small molecules.
    XenoSite Web provides an implementation of the XenoSite Cytochrome P450 Prediction Models [1]. Cytochrome P450s (CYPs) play a fundamental role in the oxidative metabolism of over 90% of FDA approved small-molecule drugs. As such, predicting the way that small molecule drugs are oxidized by CYPs can aid in the rational design of safe, effective drugs that exhibit high bioavailability.

  • yApoptosis DATABASE | SYSTEMS BIOLOGY
  • yApoptosis is an extensively-curated database dedicated for researchers working on yeast apoptosis. It is an open platform established to facilitate the organization and sharing of knowledge. It structurally collects annotated information of apoptotic genes such as pathway information, GO terms, relevant literature, and provides additional links to protein information, gene expression and interaction data. yApoptosis is a part of the broader yCellDeath project. More data and tools will be continuously added, and the apoptosis networks will be revised and updated on a regular basis.

  • ZINC DATABASE | PHARMACOLOGY
  • ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 13 million purchasable compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco
    (UCSF).

  • ZOOMA THESAURI – TOOL | ONTOLOGY
  • ZOOMA is an application for discovering optimal ontology mappings, designed to automatically map text values to ontology terms. ZOOMA performs text to ontology term mappings by operating over “repositories of mappings”. Normally, this means Bioportal, OLS or an ontology you have supplied: terms are matched to these resources based on vendor-specific search algorithms (or, reasoning and text matching over supplied ontologies). However, it is also possible to interface ZOOMA with databases – as we do at the EBI –to allow mappings to be reused whenever they’re encountered again.

  • 12th Bio-Ontologies meeting (2009) THESAURI | ONTOLOGY
  • Special issue of Journal of Biomedical Semantics with a selection of seven papers as extended versions of the original
    papers presented at the 2009 SIG. The papers span a wide range of topics including theoretical research, representation of biological and artifactual functions, an ontology for modeling biomedical experimental processes (OBI), an ontology for bibliographic referencing (CiTO), an ontology recommender web service, an approach for representation of biomedical statements (aTags), a knowledge Base for RNA structure and function, and a rule-based approach for semantic integration of heterogeneous data sources.

  • 2nd International LL symposium: New Horizons in Toxicity Prediction OTHER
  • New Horizons in Toxicity Prediction, the 2nd International Lhasa Symposium, took place on September 15th and 16th

    2010, in Leeds, UK. Now you can access the presentations/abstracts from the speakers at this event – here.