The new CoCoMac database: a community project
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1
Radboud University Nijmegen, Netherlands
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2
Textensor Limited, United Kingdom
The CoCoMac database (Collations of Connectivity data on the Macaque brain) contains neural connectivity data of the Macaque brain, obtained from 400+ published tracing studies. The database has been online since early 2000 at www.cocomac.org, and is widely used as a real-time, searchable source of connectivity data.
Keeping CoCoMac up to date requires approximately two working days per new tracing study. In practice, this means that we need to prioritize new publications based on our current research interests. To circumvent this limitation, the current project presents a new interface that allows authors and users to enter new publications into CoCoMac themselves. This has many benefits:
1. New data is added to CoCoMac at a faster pace
2. A researcher in the field can enter missing data that is crucial for his area of interest.
3. The author of a tracing study is the best person to contribute to the database, since s/he knows in detail how the data were generated.
The main issues to resolve when allowing others to manipulate the database are (1) to make sure that the data entered is correct, and (2) to guard the integrity of the database at all times.
The crucial step to achieve this has been to create two separate databases in a master-slave relationship. The first one is the data-entry database. It contains, for each publication separately, all the commands and associated data that were given by the data collator through the data-entry software. The second database is the search database. It is identical to the original CoCoMac database, and contains separate tables for different types of data to enable fast searching. The search database is regenerated from its master whenever new data has been entered.
Since the data-entry database logs all commands given by all users, it is easy to correct wrong entries. We can look at each publication, see the most recent changes, and undo them if necessary. When generating the search database, we can decide which publications are imported; we can skip articles that we haven't proofread or those that are embargoed by a review process. Different search databases can be generated in parallel for different users. The new data-entry interface is web-based, written in MySQL, PHP and JavaScript. It interacts with the server through XML requests. All information related to a single publication is conveniently displayed in an expandable tree, and all data-entry commands are given through self-explanatory forms. Form fields which contain recurring items, such as brainmaps, brainsite acronyms, macaque species etc. use temporary tables from which they read lists of suggested inputs.
As a future development, these recurring items can be tagged by manuscript authors as part of the paper submission process. To that end we are collaborating with Textensor Limited, who have developed a web-based manuscript tagging system (A.nnotate.com). Adapting the tag set to CoCoMac contents will allow us to identify publications that provide relevant further information on, e.g., a brainsite, injection method or macaque species of interest.
Conference:
Neuroinformatics 2008, Stockholm, Sweden, 7 Sep - 9 Sep, 2008.
Presentation Type:
Oral Presentation
Topic:
Live Demonstrations
Citation:
Bakker
R,
Cannon
RC,
Howell
FW and
Kötter
R
(2008). The new CoCoMac database: a community project.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2008.
doi: 10.3389/conf.neuro.11.2008.01.139
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Received:
28 Jul 2008;
Published Online:
28 Jul 2008.
*
Correspondence:
Rembrandt Bakker, Radboud University Nijmegen, Nijmegen, Netherlands, nemoABS01@frontiersin.org