Essential Requirements for Community Annotation Tools

Scientific research is inherently a collaborative task. Berkeley

Bioinformatics Open-Source Projects (BBOP) develops software to support

the work of biocurators. Our tools foster dialog among researchers to

reach a shared understanding of the underlying biology.

ESSENTIAL REQUIREMENTS FOR COMMUNITY ANNOTATION TOOLS

INHERENTLY COLLABORATIVE

Annotation tools help improve curation quality, and in many research groups

they constitute a means to introducing human curation to the annotation

process for the first time.

APOLLO NOCTUA

BBOP

Apollo supports curation of gene models for multiple organisms in one server and generates analysis-ready data as well as progress reports. We make continuous improvements to support the needs

of the growing research community that forms our user base.

Apollo is a collaborative genome annotation editor. It is instantaneous, web-based, and built on top of

JBrowse.

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ANNOTATION ACROSS SCAFFOLDS

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1. User-created Annotations2. Evidence Tracks: Experimental Data, Alignments3. Annotator Panel

Noctua directly models information as a graph, escaping many of the pitfalls of more tabular modeling. A rich, interactive and collaborative

interface allows users to assemble graphs to represent biological knowledge including aspects such as references and evidence.

Noctua is a modern web-based application and stack for modeling complex biological processes.

Immediate communication between curators through parallel chat mechanisms.

Real time updates to allow geographically dispersed curators to conduct joint, simultaneous efforts.

Well supported history mechanisms providing the ability to comment on versions, browse versions to see different edits and commentary, and revert to earlier versions.

Rigorously documenting the experimental or inferential basis for all of the annotations that are made, with credit assigned through citations.

Offering incentives for adoption, such as facilitating the publication process.

Providing different levels of permissions for users and administrators, for example so that a curator might “doodle” within their own work area before releasing their version for feedback from others.

Functional stability and ease of migrating forward when new software is released.

Prompt responsiveness to users’ requests and informative documentation, and dedicated resources for training and user support, from online seminars to video tutorials to repositories with teaching materials.

And, most importantly, a publishing mechanism, such that biocurators and other contributors receive credit for their insights and contributions to our collective understanding of biology.

Monica Munoz-Torres1, Chris Mungall1, Nathan Dunn1, Seth Carbon1, Heiko Dietze1, Nicole Washington1, Jeremy Nguyen1,

Paul Thomas2, Suzanna Lewis1.1 Environmental Genomics and Systems Biology Division,

Lawrence Berkeley National Laboratory, Berkeley, CA2 Keck School of Medicine, Department of Preventive Medicine,

University of Southern California, Los Angeles, CA

Apollo is funded by NIH grants 5R01GM080203 from NIGMS, and 5R01HG004483 from NHGRI. Also supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

Noctua also presents a complete set of tooling for data extraction and

integration.

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