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It is vital that we properly organize and reference the body of similar work so that we can most easily gain the most value from that work.


MetaBase is by no means unique. There are many related resources, falling into two broad categories:

  • Firstly, there are several other 'BioWiki' projects. Like MetaBase, these projects use the tremendously successful MediaWiki [1] software platform to provide user contributed content to the biological community. See the BioWiki tab (below).
  • Secondly, there are several other 'databases of biological databases'. Like MetaBase, these projects aim to provide a list of all the most important biological databases and data resources available on the internet. See the MetaDatabases tab (below).


Use the tabs below to see more content in each category.

[edit]

Projects with a similar philosophy.

The most successful collection of user contributed content is Wikipedia [2]. The success of Wikipedia is intimately related to the success of the MediaWiki software platform [3], leading to a proliferation of wikis, including several BioWiki projects. However, Wikipedia is still a very important resource for biologists. Many of the databases in MetaBase also have articles in Wikipedia, see the Articles also in Wikipedia category.

Some of the most important and interesting BioWiki projects are listed below (for a comprehensive list, see the BioWiki database on Bioinformatcs.Org):

The Molecular and Cellular Biology 'WikiProject' (part of Wikipedia) 
This project aims to better organize information related to molecular and cellular biology in Wikipedia. Some pages are specifically relevant to MetaBase include: the bioinformatics databases category and the bioinformatics software category. More information...
OpenWetWare (OWW) 
An effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology and biological engineering. Established in 2005, OWW is one of the oldest dedicated BioWikis More information...
The Bio Community Cluster (BiO.CC) 
A wiki farm where many 'openfree' bio-sites may be added, constructed, evolved and networked. More information...
The Bioinformatics.Org/Wiki 
A collection of articles on topics related to bioinformatics. For example, the bioinformatics FAQ, bioinformatics books, bioinformatics software, and bioinformatics topics.
EcoliWiki 
The goal for EcoliWiki is to generate community-based pages about everything related to E. coli. K-12, its phages, plasmids, and mobile genetic elements. Of particular relevance to MetaBase is the list of databases related to E. coli.. More information...
WikiPathways 
An open, public platform dedicated to the curation of biological pathways by and for the scientific community. More information...
SNPedia 
A website to share information about the effects of Single Nucleotide Polymorphisms in your DNA, citing peer-reviewed scientific publications. More information...
PDBWiki 
A community annotated knowledge base of biological molecular structures. More information...
Proteopedia 
An educational resource for proteins and other molecules. More information...
WikiProteins 
A collaborative project to annotate information about Proteins. More information...
MyBio 
A community-built directory of tools, databases, protocols and other web resources for life sciences researchers. In particular, MyBio maintains an archive of biological databases, making it very similar to MetaBase. More information...

Projects with a similar scope.

The Molecular Biology Database Collection 
A public on-line resource that lists the databases described in Nucleic Acids Research, together with other databases of value to the biologist. More information...
The Health Sciences Library System (HSLS) Online Bioinformatics Resources Collection (OBRC) 
Contains annotations and links for 1,746 bioinformatics databases and software tools. More information...
The Bioinformatics Links Directory 
Features curated links to molecular resources, tools and databases. More information...
Common Access to Biotechnological Resources and Information (CABRI) 
An online service where users can search a number of European Biological Resource Centre catalogues. The catalogues may be searched independently, or as one, and the located materials ordered online or by post. More information...
The Database of Biological Database (DBD) 
Consists of 1,200 Database entries covering wide range of databases useful for biological researchers. More information...
The Database of Databases (DoD) 
Links to all molecular biology databases that appear in the Nucleic Acids Research database issue. More information...
BioDBCore 
A community-defined description of the core attributes of biological databases overseen by the International Society for Biocuration in collaboration with the BioSharing forum. More information...
MetaBasis 
A database system for the effective management of metadata concerning software tools and databases in the field of Bioinformatics. The system contains 3,229 published Bioinformatics Tools and Databases. More information...
BioWareDB.org 
An attempt to collect an exhaustive database of links to the vast amounts of freely available and commercial bioinformatics software. More information...
Biomed Cetral Databases 
A catalog of online databases containing more than 1,100 sites covering a wide range of biomedical topics from Alzheimer disease to zebrafish anatomy. More information...
OReFiL 
An Online Resource Finder for Lifesciences. More info...
The National Institute of Standards and Technology (NIST) Data Gateway 
Provides easy access to many of the NIST scientific and technical databases. These databases cover a broad range of substances and properties from many different scientific disciplines. More info...
See also 
The following dynamically generated list of MetaBase resources in the 'database of databases' category.
BioWareDB.org, Bioinformatics Links Directory, CABRI Common Access to Biological Resources and Information, DBD: Database of Biological / Bioinformatics Databases, DoD: Database of Databases, MetaBase, Molecular Biology Database Collection, NIST, OBRC: Online Bioinformatics Resources Collection, The Database Issue of Nucleic Acids Research.

Projects related to the systematic archival of biological resource metadata.

BioCatalogue 
Provides a curated catalogue of Life Science Web Services. More information...
Biositemaps 
Technologies to address locating, querying, combining, and mining biomedical resources. More information...
Biomedical Resource Ontology 
A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches. More information...
CASIMIR Database Description Framework (DDF) 
Allows resources to describe key technical metadata in a formalised way. The aim of the DDF is to allow researchers to discover which databases support the standards and interfaces they require. More information...
EDaM Ontology 
EDaM (EMBRACE Data and Methods) is an ontology of general bioinformatics concepts, including topics and data types, formats, identifiers and operations. EDaM provides a controlled vocabulary for description in semantic terms of biological resources. More information...
The Neuroscience Information Framework (NIF) 
The NIF Registry catalogs web accessible neuroscience research resources and is searchable by content and resource type. More information...
Pathguide 
Pathguide contains information about 325 biological pathway related resources and molecular interaction related resources. More information...
ELIXIR 
To construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society. More information...
European Model for Bioinformatics Research and Community Education (EMBRaCE) DEAD 
The EMBRACE Service Registry was a collection of life-science web services with built-in service testing. This system will be merged into the BioCatalogue. More information...
BioSapiens 
A European Virtual Institute for Genome Annotation. More information...
ENFIN 
Committed to providing a Europe-wide integration of computational approaches in systems biology. More information...

This section is largely unstructured. You can help!

Hard to categorize

The Database of Databases of Biology Databases 
There are biology databases. And then there databases of biology databases. This is a database of those databases of biology databases! (A meta-meta-database!)
  • The BioForum for discussion of (amongst other things) databases and web-resources.
  • The Biologistonline is a designed to give Biologists the tools necessary to study life. From students to Phd.'s there is something for everyone here. With The Biologistonline you can: ... http://thebiologistonline.com/community/

Hard to fathom

To sort

  • Commercial GeneGo MetaBase™ : Arguably, the most comprehensive manually curated database of mammalian biology and medicinal chemistry data available today. http://www.genego.com/metabase.php


Open Chemistry

ChemXtreme 
Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme.

Links to literature relating to MetaBase

Time to Organize the Bioinformatics Resourceome [4] 
"We suggest that the full set of bioinformatics resources - the "resourceome" should be explicitly characterized and organized. A hierarchical and machine-understandable organization of the field, along with rich cross-links (an ontology!) would be a useful start. It is likely that a distributed development approach would be required so that those with focused expertise can classify resources in their area, while providing the metadata that would allow easier access to useful existing resources."


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