From MetaBase

Contents 1 Paper Text 2 Title: Metabase: the database of biological databases 2.1 Abstract 2.2 Introduction 2.3 Database Description 2.3.1 Current Status 2.3.2 Database Contents 2.4 Future directions 3 EOP 3.1 See Also 3.1.1 Useful Links

[edit] Paper Text

Paper text goes here...

IMPORTANT: See the discussion page before anything else!

[edit] Title: Metabase: the database of biological databases

[edit] Abstract

Metabase is an international community based database that aims to list and guide all the commonly used biological databases in the world.

[edit] Introduction

Harum...

• The future of the internet and wiki?
• Collaboration & Web 2.0?
• The future of science?

Related work...

[edit] Database Description

At the most basic level, MetaBase is a user-contributed list of all the biological databases available on the internet. For this reason, the MetaBase can be considered a 'database database'.

In detail, MetaBase aims to fulfil the following list of requirements;

• As a basic requirement, the MetaBase will contain a list of databases, URLs and descriptions of the most commonly used biological databases currently available on the internet.
• The MetaBase should be flexible, allowing many users to contribute, update and maintain the data. The data management software should be flexible, allowing a continuous growth of the range and scope of databases and database information.
• The MetaBase should be 'classifiable'. That is to say that it should not contain just one fixed database classification scheme, but many. Potentially any user could create his or her own classification of databases according to any criteria, and those classifications should be available to everyone.
• The MetaBase should be extensible, allowing, for example, scientific papers to be linked to the databases through a variety of relationships.
• The MetaBase should provide an up-to-date source of biological database information, as well as tools for gathering database usage and quality information from the biological community.
• The MetaBase should facilitate more communication between the database developer and user communities.
• Potentially the MetaBase could be used as a source of 'genuine' meta-data for data integration projects.

This list of requirements should not be considered static. The MetaBase aims to be a flexible, user-driven (user-created) resource for the biological database community. The above aims can be constantly revised to meet new requirements as they arise.

[edit] Current Status

The above list of requirements was found to fit very well with the feature set provided by MediaWiki. For this reason, the MetaBase has been implemented using MediaWiki (version 1.10.0) and is currently hosted on BiO.

More design details here.

[edit] Database Contents

More counts here.

The initial release of MetaBase was derived entirely from the content of the Nucleic Acids Research (NAR) 2007 Database Issue. Specifically, each MetaBase database page was 'seeded' with text from the 'Database Summaries' cite provided by NAR. Because of the way this text is licensed, its use is subject to several restrictions that in turn restrict the complete use of MetaBase. Although the NAR Open Access policy allows us to use the text, the following two important stipulations apply;

  1. The text for each database must be reproduced verbatim and in its entirety.
  2. The use of the text is to be strictly non-commercial. 

[edit] Future directions

Something from the projects section (see Main Page).

[edit] EOP

[edit] See Also

[edit] Useful Links

• -> Nucleic Acids Research -> For Authors -> SUBMITTING TO THE ANNUAL DATABASE ISSUE

NOTE: New submitters should follow the guidelines set forth below for submission. The deadline for new articles describing databases not previously described in NAR is August 15. Authors MUST contact Dr Alex Bateman at nardatabase@mrc-lmb.cam.ac.uk to check the suitability of their proposed submission by July 1st at the latest. Manuscripts should not be submitted before June 1st.

• NOTE: Submission
  • Authors should submit their manuscript electronically through Manuscript Central (http://mc.manuscriptcentral.com/nar). The manuscript MUST be uploaded as a .doc or .rtf file. It must NOT be uploaded as a .pdf file.
  • Authors should produce a brief description of their database. Again, this description should concentrate on the factual content of the database and provide sufficient information so that the reader can easily access and obtain information from the database. New submissions to NAR are typically 4-5 printed journal pages in length, but authors are urged to be succinct in their writing.
  • The online version of the Database Issue affords the authors the opportunity to provide readers with supplementary data. Authors are encouraged to provide online-only supplementary data to amplify on various aspects of the use of the database or the content of the database. A good way to organize this supplementary data would be to include, within the main text of the printed article, a short table of contents (one line per item) describing the supplementary data. Each topic could then be expanded as appropriate within the supplement. Authors are encouraged to be innovative in their use of such supplementary data, taking advantage of the fact that electronic material, unlike the printed text, does not need to be static. All supplementary data must be available at the time of submission, for editorial review.
  • Authors should try to use the database name as the first word in the title and should include within the article a valid URL through which the database can be accessed. The database must be completely functioning and available for review at the time of submission. If the database has its own homepage, the URL must be included in the abstract and may be repeated within the text of the article. The home page should not be used as a figure in the main text article to be printed, but a representative screen dump showing the output of a particular query would be allowed. The final article will contain a hotlink to the homepage of the database.
  • Citations to other databases should be to the most recent published description. References to URLs are not permitted.
  • References must be in the correct journal format and should be cited in the text by sequential number only, in order of appearance, and listed numerically in the References section. Manuscripts 'submitted' or 'in preparation', unpublished results, and personal communications should not be cited.
  • Authors must supply the names, institutes and email addresses of six suggested referees. They should be scientists working independently (i.e. not a recent collaborator) in areas similar to your own who have relevant expertise, such as those included in your reference list.
  • For more specific information, please consult the general Instructions to Authors.
  • If your paper is accepted for publication, you will receive additional information on submitting an entry to the Molecular Biology Database Collection.
  • Not all databases can be included in the Database Issue as individual articles. If your manuscript is not accepted for publication, but the database is deemed appropriate for inclusion in the Molecular Biology Database Collection, you will receive additional information on how to submit your entry to that collection.
  • Databases must be freely available to all via the web and not be password protected. Authors are encouraged, but not required, to make the contents of their databases freely available as flat or relational files upon request.
  • Authors should include a section on availability of the database, which includes details of methods of access as well as the under what terms of license the data are available.