Tools for data sharing
Software server allows users to share and edit geospatial metadata and to link them to on maps that are available on line in a search interface. Metadata are based on the ISO 19115 and ISO 19139. It is interoperable with any maps server provided in WMS and CSW formats. Compliant with the Z39.50 and OAI-PMH protocols.
Morpho Metadata Editor
Application designed to facilitate the creation of metadata so that scientist can easily locate and determine the nature of a wide range of data sets. It interfaces with the Knowledge Network for Biocomplexity (KNB) Metacat server.
Virtual research environments — a web-based content management software (based on Drupal) which facilitates the organisation and publication of biodiversity data (mobilisation, structuring, linking and dissemination of taxon-centric information)
An online resource for regularly updated, quality checked and annotated ribosomal DNA sequence data for kingdom Fungi.
The Barcode of Life Data Systems (BOLD)
Supports the generation and application of DNA barcode data. Accepts new submissions (incl. submission of primary specimen data, images, trace files, and nucleotide sequences) and provides tools for third-party annotations to DNA barcodes by tagging and commenting options.
The 16S rRNA Gene Database and Tools (Greengenes)
Provides access to the 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading.
TDWG Access Protocol for Information Retrieval. Its purpose was to unify the DiGIR and BioCASe protocols and make the protocol independent of certain schemas.
Sequence Read Archive (SRA)
Stores raw sequencing data from the next generation of sequencing platforms (e.g. Roche 454 GS System, Illumina Genomy Analyzer, etc.).
ReFindit provides an easy reference search engine, based on a simple interface, allowing to browse millions of bibliographic references and metadata stored in CrossRef, PubMed, RefBank, Mendeley and GNUB. The searched references may be used for different purposes, for example direct import and citation in manuscripts via the Arpha Writing Tool, conversion in some 600 journal citation styles and download in widely accepted bibliographic metadata standards.
ARPHA Publishing Platform
ARPHA stands for: Authoring, Reviewing, Publishing, Hosting and Archiving, all in one place. The platform aims at increasing the proportion of structured text and data within the journal article's content, so as to allow for both human use and machine readability. This is the first ever end-to-end, entirely XML-based solution in the journal publishing industry.
Biodiversity Data Journal
A scholarly journal by Pensoft using an innovative narrative (text) and data integrated publishing workflow to stimulate mobilisation, review, publication, storeage, dissemination, interoperability and re-use of biodiversity data.
ARPHA Writing Tool (AWT)
This online authoring tool is developed by Pensoft to provide a rich collaborative writing, peer-review and editing environment for research manuscripts. It powers plugins for both automated import and export of metadata from and to domain specific repositories, as well as for direct manuscripts import via XML/API.
Data Publishing and Dissemination Toolbox
The EU BON’s Data Publishing and Dissemination Toolbox (DPDT) is a set of standards, guidelines, recommendations, workflows and tools designed to ease scholarly publishing of biodiversity-related data. The core element of the EU BON’s Data Publishing and Dissemination Toolbox (DPDT) is the ARPHA Publishing Platform developed by Pensoft.
DSpace is an open source digital object management system, useful for managing arbitrary digital objects, such as data files. As distinct from Fedora Commons (managed by the same organisation – DuraSpace), DSpace comes with a usable user interface and is relatively usable “out of the box”.
Metacat: Metadata and Data Management Server
A repository that helps scientists store metadata and data, search, understand and effectively use the data sets they manage or those created by others. A data provider using Metacat can become DataONE member node with a relatively simple configuration.
Web application that supports publication of biodiversity data to the GBIF network using pre-configured Microsoft Excel spreadsheet templates. Two main data types are supported: i) occurrence data as represented in natural history collections or species observational data and ii) simple species checklists.
Online service to create, manage, share, analyse and mobilise biodiversity data. Data types cover ecology, taxonomy, metagenomics, nature conservation, natural history collections, etc.
Bibliography of Life
A platform consisting of three integral tools, RefBank and ReFindit and Biosystematics Literature Repository based at ZENODO/CERN. RefBank is the place to store, parse, edit, and download bibliographic references, ReFindit is designed to discover and download references from a wide range of open access online bibliographies
Species Observation System
A web-based, freely accessible reporting system and data repository for species observations, used by citizen scientists, scientists, governmental agencies and county administrations in Sweden and Norway. The system handles reports of geo-referenced species observations of almost all major organism groups from all environments, including terrestrial, freshwater and marine habitats.
Comprehensive online resource for regularly updated, quality checked and aligned ribosomal RNA sequence data for all three domains of life (Bacteria, Archaea and Eukarya).
Server software written in Java that allows users to share and edit geospatial data. GeoServer is the reference implementation of the WMS, WFS and WCS standards of the OGC, as well as a high performance certified compliant WMS.
Genomic Standards Consortium (GSC)
Standardising the description, exchange and integration of molecular/genomic data.
Research Ideas and Outcomes (RIO) Journal
RIO aims at making better use of the vast effort spent on writing and evaluating research proposals and other valuable products of the research cycle. It harnesses the full value of investment in the academic system by registering, reviewing, publishing and permanently archiving a wider variety of research including research ideas, grant proposals, software, data, data and software management plans, research and review articles, policy briefs, and more.
Dryad Digital Repository
The ‘Dryad Digital Repository‘ is a curated resource providing a general-purpose location for a wide diversity of data types. Dryad's mission is to make the data underlying scholarly publications discoverable, accessible, understandable, freely reusable, and citable for all users.
European Nucleotide Archive (ENA)
Captures and presents information relating to experimental workflows that are based around nucleotide sequencing. INSDC forms the most comprehensive database for all molecular data types and linked metadata.
The International Ecological Information Management System (DEIMS) is a Drupal open-source, collaborative platform, that provides a web interface for scientists and researchers' networks, projects and initiatives with a metadata management and data sharing system.
Commercial software storing data, such as Microsoft Access, Microsoft SQL Server, and Oracle, and open source tools such as MySQL, PostgreSQL, and SQLite.
A scholarly journal which provides a forum for studies in the field of ecology and sustainability. In addition to conventional research papers, the journal welcomes contributions documenting the entire research cycle, including data, models, methods, workflows, results, software, perspectives and policy recommendations.
Pensoft Taxon Profile
The Pensoft Taxon Profile (PTP) is a web-based harvester that automatically links any taxon name mentioned within a text to external sources and creates a dynamic web-page for that taxon.
The Integrated Publishing Toolkit (IPT) is a free open source software tool written in Java that is used to publish and share biodiversity datasets through the GBIF network.
Plazi Treatment repository
Plazi is an association supporting and promoting the development of persistent and openly accessible digital taxonomic literature.
A software and transnational network of biological collections of all kinds. BioCASE enables widespread unified access to distributed and heterogeneous European collection and observational databases using open-source, system-independent software and open data standards and protocols
XML-based protocol to implement queries to distributed data providers. It is modelled after the Z39.50 protocol. Supports several operations such as inventory of information resources on a provider, download to resource metadata, and queries to the full data.
DataONE Generic Member Node
Is a python reference implementation of a complete (Tier 4) member node to DataONE. Where an existing data repository wishes to become a DataONE member node, the GMN is a tool that can be used to adapt the repository’s existing software.
Data Access Protocol-compliant servers (DAP)
REST web service based protocol designed for science data. There are multiple software packages which implement DAP, e.g. OPeNDAP Hyrax and THREDDS. There is current development to make Hyrax and THREDDS DataONE-enabled.
Microsoft Excel, DataUp and open source tool Libre Office are a software packages that enables the creation of spreadsheets or forms, provides simple data comparison and analysis tools, and creates graphs.