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One of the objectives of the PhyloFacts project is to eventually provide detailed annotation of every significant gene family in the universal proteome. As more complete genomes from across the tree of life are made available for inclusion, an increasing fraction of new sequences will fit into already identified protein families. Although an exact value is unknown, we offer a very rough estimate that most proteins from most eukaryotic organisms will able to be directly classified into approximately 100 thousand protein families.
As the universal proteome coverage is completed, the challenge will shift from identifying protein families to understanding them. Anticipating this transition, PhyloFacts has been designed to enable and encourage community participation in parallel with automated methods in the analysis and annotation of the protein families.
To the extent that computational methods are comparable to expert attention, they have been utilized: constructing multiple sequence alignments, trees, HMMs, finding homologous solved structures, identifying putative functional subfamilies, detecting GO enrichment, interaction patterns, key residues, and so forth. By providing such data along side embedded visualization, data manipulation tools and a convenient means for submitting annotation, it is hoped that we have not only provided a space for the human mind to perform the abstract pattern analysis it is so singularly effective at, but also a means for those minds to leave a record of what they have gleaned for the benefit of those that come after them.
There are three basic tiers at which community editorial capacity of PhyloFacts protein families:
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Flag Now
Check below for links to automatically detected interesting or suspect entries:
odd domains
odd species
odd annotation
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1: Flagging
Any visitor to the site may add a flag to any sequence, alignment, or protein family by clicking the ubiquitous comment symbol, shown to the right. On the first flagging, the user will be asked to provide a minimal amount of information and password, as well as pass a CAPTCHA. On subsequent visits they enter their password next to their comment, or have their browser remember it. The user also has the option to keep a local PhyloFacts authentication cookie, if they should so desire. Flagging is most convenient for bringing something to a curator's attention, providing links to a relevent publication or other source of current relevent research, or otherwise providing information that may be of use to other users.
2: Curation
Although convenient, flagging offers a somewhat limited avenue of annotation, and still requires the attention of a dedicated curator to review and take action on the flags to incorporate them into the permanent resource record. For many users that primarily access the site to recover information on a few records this is ideal, but some users might desire a more thorough approach to annotating protein families. curator status is obtained by submitting a request that includes basic information on background, affiliation, contact information, and the like. Once accepted, the curator will receive access to many book record modification tools, allowing the curator to change the name, add literature, provide detailed description of the function, and other activities. A researcher that spends a lot of time using certain PhyloFacts books, and desires to improve them might make an ideal curator.
[application available soon]
2: Editorial
The final tier to PhyloFacts annotation provides full editorial capability to the user. The user can build protein families, obsolete existing ones, and change any aspect of current content. Full editorial capacity would be appropriate for a dedicated specialist with some experience as a PhyloFacts curator.
[application available soon]
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