Abstract
The Human Proteome Project is moving into the next phase of creating and/or reconsidering the functional annotations of proteins using the chromosome-centric paradigm. This challenge cannot be solved exclusively using automated means, but rather requires human intelligence for interpreting the combined data. To foster the integration between human cognition and post-genome array a number of specific tools were recently developed, among them CAPER, GenomewidePDB, and The Proteome Browser (TPB). For the purpose of tackling the task of protein functional annotating the Gene-Centric Content Management System (GenoCMS) was expanded with new features. The goal was to enable bioinformaticans to develop self-made applications and to position these applets within the generalized informational canvas supported by GenoCMS. We report the results of GenoCMS-enabled integration of the concordant informational flows in the chromosome-centric framework of the human chromosome 18 project. The workflow described in the article can be scaled to other human chromosomes, and also supplemented with new tracks created by the user. The GenoCMS is an example of a project-oriented informational system, which are important for public data sharing.
Highlights
In this paper we report observations from the Chromosome-Centric Proteome Project (C-HPP).The chromosome-centric approach assumes a deep proteomic study of an individual chromosome, which implies the integration of post-genomic data in a geno-centric mode
What usually makes the leading investigators choose to preserve these data locally, instead of uploading into the public domain? Superficially, the data is preserved because of the potential usefulness for the data producer. There is another significant reason to share not through the public resources, but instead via local databases. It is an IT-development in the domain of data, on how to organize the process of generation of the data we described in the gene-centric workflow, where each block was implemented by one of the teams participating in the chromosome 18 (Chr18) proteome project
There is the lack of a resource which could be universally useful for describing an abstract proteomic experiment
Summary
The chromosome-centric approach assumes a deep proteomic study of an individual chromosome, which implies the integration of post-genomic data in a geno-centric mode. Bioinformatics tools enable us to process the raw data acquired from many of the experiments. We witness the birth of new bioinformatics which serve as an integrative technological chain between data acquisition, data processing, and data interpretation. The chromosome-centric approach is key to working within the data-intensive domain [1]. The centricity of the chromosome assists in coping with increasing amounts of data, such as the geometrical growth of the human RNA-seq in the National Center for Biotechnology Information (NCBI) sequence read archive. The volume of the proteome data is increasing more slowly, but still sufficiently—almost twice a year
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