Annotare is a forms-based software for annotating biomedical investigations and resulting data in MIAME (Minimum Information About a Microarray Experiment). It supports biomedical ontologies, contains standard templates for common experimental types, and includes a design wizard for creating your own forms.

• Installation instructions

CEDAR Workbench is an open source tool to manage metadata for any field of study, using rigorous semantic principles if desired. It allows users to specify templates using a UI (like survey forms in Google Forms or Survey Monkey), then to fill out those forms efficiently using drop-down menus, help tips, and intelligent suggestions. Templates and metadata can be shared with other users and groups. Metadata also can be downloaded in JSON-LD, simple JSON, or RDF, or exported to connected repositories, which can be integrated using the full API suite.

• Getting started

ISA Creator is an open source, stand-alone application that assists with planning and describing experiments and facilitates export and import of data directly to and from some public repositories. Additional tools are available in the ISA-Tools software suite for parsing ISA-Tab into R data structures and for parsing PERL and Python for ISA-Tab. ISA-Tab is the required format for publishing data in Nature Publishing's Scientific Data journal. This software creates separate descriptive files for your experimental files.

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• User manual

Morpho allows you to describe ecological experiments in EML (Ecological Markup Language) and to create a catalog of data and descriptions that you can query. It includes an interface to the Knowledge Network for Biocomplexity (KNB) for sharing, querying, viewing, and retrieving data. 

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OMERO is repository software for importing, viewing, organizing, describing, analyzing, and sharing microscopy images from anywhere you have Internet access. It includes the ability to create user groups with different permissions for sharing data.

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• Documentation

OntoMaton provides ontology searching and automated tagging via NCBO's Bioportal of biomedical ontologies within Google spreadsheets. This tool is best for biomedical research. OntoMaton is part of the ISA-Tools suite. Annotations are generated within your tabular data file.

• Installation
• Video tutorial

RIghtField is an open source tool that allows searching and selecting of ontology terms for any field of study from within Microsoft Excel. RightField allows you to assign a pre-determined list of options to a particular cell within the spreadsheet. All annotations are embedded within the spreadsheet. The user can select from the NCBO's BioPortal ontologies or import an ontology from a URL or your local machine.

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• User guide