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https://github.com/wurmlab/afra

Genome Annotation for the Masses
https://github.com/wurmlab/afra

crowdsourcing curation education gene-prediction

Last synced: about 2 months ago
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Genome Annotation for the Masses

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README 

          
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## Afra: crowdsourcing gene feature annotation



Genomes of emerging model organisms are now being sequenced at [low cost](http://www.genome.gov/images/content/cost_genome.jpg).

However, obtaining accurate gene predictions remains challenging.  Even the

best gene prediction algorithms make substantial errors, leading to further

erroneous analysis. Therefore, many predicted genes need to be visually

inspected and manually curated ([Yandell & Ence](http://www.nature.com/nrg/journal/v13/n5/full/nrg3174.html)); this can be infeasible when working with thousands of genes from multiple organisms.



Inspired by crowdsourcing approaches and platforms including

[Foldit](http://fold.it/), [Galaxy Zoo](http://www.galaxyzoo.org/) and

[Crowdflower](http://www.crowdflower.com/), we are developing Afra to recruit

additional gene feature curators.  This should help dramatically increase

the quality of gene curations available for newly sequenced genomes. In the

long-term we aim to recruit contributors among members of the general public.

However, gene curation requires large amounts of specialist knowledge and

overcoming a steep learning curve. While we are working to reduce the steepness

of the learning curve via interactive tutorials and support forums, genome

curation is not yet easily accessible to all. Thus in a first instance we are

recruiting curators among biology students. They perform curations as part of

their courses aiming to understand gene structure and/or challenges with gene

identification and gene prediction.



### Current status



Users login to their dashboard using their Facebook account, where they are

presented with documentation, guided tutorial exercises, and curation challenges which include "Curate" buttons.

Each curation challenge invites user to contribute towards a different curation project.



![user dashboard](www/img/readme/dashboard.png)



Clicking 'Curate' sends the user to a JBrowse-derived WebApollo-like curation interface

focusing on a single gene model and showing all available tracks of

evidence for this gene model. The user starts by dragging one of these

models (typically the consensus gene model) to the edit track and can

then edit this gene model.



![curation interface](www/img/readme/curate.png)



Users may refer to the tutorials or seek help on our forum using the 'Help &

Support' link at the top. A simple step by step guideline to curation is always

available in a sidebar that folds to the right.



#### Behind the scenes



Afra imports a GFF file of predicted gene models and creates a prioritized list of "curation tasks"

based on expected curation difficulty; the administrator can additionally prioritize specific genes

for a specific curation project. Each gene prediction is presented to four

independent users/curators. Each curator independently examines the gene model

and may propose revisions or add comments (e.g., if there is insufficient

evidence to curate).



For each gene prediction, submitted gene models are then automatically compared:

if all users propose the same changes to a gene model, these changes are

considered to be correct. If gene models proposed by different curators

disagree, the different gene predictions are shown to several more experience

curators who submit their curation in turn. If gene models proposed by the more

experienced curators disagree, all predictions are shown to an even more senior

curator who makes a final verdict.



### Roadmap



![at work](www/img/readme/at-work.png)



* ~~Annotation editing.~~

* ~~Prioritized redundant task distribution~~

* ~~Basic user dashboard.~~

* ~~Simple, non-interactive tutorials.~~

* ~~Obtain curations from eight QMUL MSc students.~~

* ~~Obtain contributions from 20 of undergraduate students.~~

* ~~December 2014: Simple editor synchronization between two tabs/windows.~~

* ~~December 2014: Improve annotation editing experience. Make it more intuitive.~~

* ~~December 2014: Basic automated testing of annotation editing functionality.~~



Todos:

* Improve page load times.

* Partially done genome dashboard: Overview of contributions per genome. How many curations. How many pass auto-check.

* Comments on curations.

* Extensive automated testing of annotation editing functionality.

* Improve annotation editing performance.

* Interactive tutorial.

* Roll out to 200 first year students learning about gene structure ... and the inadequacies of Bioinformatics algorithms.



### Contributions are welcome



We welcome contributions of code, curations, or documentation. Find us on

[Gitter](https://gitter.im/yeban/afra) to discuss how you could best help.



Our [Wiki](https://github.com/yeban/afra/wiki) details setting up a

development environment using Docker.



### Contact



Please [email](mailto:a.priyam@qmul.ac.uk) if you:

* would like a demo

* would like to use Afra in your institution to help teach students

* have any other questions



---





Afra is Copyright (©) 2013 Queen Mary, University of London.




Parts of Afra are a derivative work of JBrowse and WebApollo which are respectively copyright (c) 2000-2006 The Perl Foundation and copyright (c) 2010 Regents of the University of California.