Bio wikis. Paolo Romano Bioinformatics, National Cancer Research Institute, Genova
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1 Bio wikis Paolo Romano Bioinformatics, National Cancer Research Institute, Genova
2 Outline o Wiki systems: aims and technologies o Working with wikis: practical issues for setting up and contributing o Specific aims and issues of wikis for biology o Examples of wikis for biology and specific features and objectives 2
3 Aims of Wiki systems for biology Specific aims of wikis for biology: o Collaborative development and sharing of documentation o Collaborative annotation of database contents (external to the database) o Collaborative update of database contents 3
4 Aims: development of documentation o One of the basic aims of wiki systems o It allows to build collaboratively and share: o o o o o procedures, data, experiences, news, various information o Motivation: high quality expertise and interests on special topics are distributed o Objective: high quality Summa biologica on a given topic, equivalent to a sectorial encyclopedia 4
5 Aims: annotation of database contents o Motivation: an extended and accurate curation of databases is extremely difficult o Objective: allow users of resources to contribute their expertise, experiences, observations and results of experiments o The contents of the database are therefore collaboratively annotated o Users can control this extended curation and correct possible errors o Databases are left unchanged 5
6 Aims: updating database contents o Motivation: Databases are hard to maintain and curate accurately o Objectives: update databases on the basis of users contributions o Problems: o how reliable are users contributions? o how to capture annotations provided as a text (Wiki site) o how to trasfer this information into the database? o Procedures should be implemented providing: o o o o a way to assess users contributiosn a set of Wiki pages created from the database a tool to extract data from annotations a tool for adding this data to the database 6
7 Aims: a genome example o GenBank can be thought of as an electronic library o Submitters own records contents o GenBank cannot undergo extended annotation, reannotation, error removal unless owners request/agree o As a consequence, Genbank is not up-to-date o A wiki built by a community of experts could serve this aim: o re-annotation of records (sequence, function, ), o links to documental information and sites, o up-to-date data Salzberg SL: Genome re-annotation: a wwiki solution? Genome Biology 2007, 8:102 7
8 Issues with Wiki systems for biology o Authoritativeness of contributions and of sites: how to assess quality? o Acknowledgement of users as a way to stimulate contributions: how to stimulate quality additions? o Authorships management and reward: how to keep information on authors and assign these contributions a scientific production value o Special features for contents: how to manage the many, different data types? 8
9 Issues: authoritativeness o Quality of contributions is essential o Contributions by end users is usually considered not adequate o Achieve a quality of contributions comparable with professional annotation at service centers (EBI, ) o Example of Wikipedia success may help (?) o Possible solutions: peer-evaluation of contributions, identification of users 9
10 Issues: acknowledgement o It is needed to stimulate good contributions o How to attract best experts in the field? o Which kind of reward can be assigned to best contributors? o Identification and citation: is this enough? o Benefits (subscriptions to services, journals, )? 10
11 RNBIO participation Italian Network of Oncology Bioinformatics web site Based on Plone + Zwiki 22 members can create and edit pages A small fraction did it, even for the simplest tasks Contents News Events Public docs Newsletters Private docs Overall Pages Users
12 Issues: authorships management o Authorships assignment is a form of acknowledgement o Contributes to define reliability of information, while providing authors due credits o Enables peer-review: authors can rate each other an automatic reputation system can be implemented o Allows a knowledge base to evolve into a rigourous scientific tool via continual revision and peer-review o How to combine collaborative (and altruistic) features of wiki systems with authorships? Hoffmann R: A wiki for the life sciences where authorship matters, Nature Genetics
13 Issues: features for different contents o Textual information is only a small part of biological data o Biological data types are numerous and heterogeneous, depending on the domain o How to cope with the different data types? o images, o plots, o diagrams o Adaptation of wiki systems is needed 13
14 Many bio-wikis available Many sites already available: o Brede Wiki Results for neuroimaging studies. o Ecoliwiki - Comprehensive information on Escherichia coli o GenWiki Genealogy resource for German-speaking people o GONUTS GO Normal Usage Tracking System: a wikibased GO term browser. Allows community curation of GO annotations for any gene. o MetaBase Biological databases o Metagenes Metagenomic DNA sequences o PDBWiki Macromolecular structures From Gene Wiki portal 14
15 Many bio-wikis available (cont d) Many sites already available: o Proteopedia Annotation of protein structures and other biomolecules o SNPedia Genetic polymorphisms o SubtiWiki Genes of Bacillus subtilis o TOPSAN Annotation of protein structures o WikiGenes Gene wiki with authorships attribution o WikiPathways Curation of biological pathways o WikiProteins Protein wiki for structured data o ZebrafishGenomeWiki Community annotation of the Zebrafish genome From Gene Wiki portal 15
16 Introduction to bio-wikis A quick introduction to: o Gene Wiki o WikiGenes o WikiPathways o WikiProteins See tomorrow Alex Bateman s keynote RNA WikiProject: Community annotation of RNA families 16
17 Gene Wiki: references o Gene Wiki iki o Huss JW III, Orozco C, Goodale J, Wu C, Batalov S, et al. (2008) A Gene Wiki for Community Annotation of Gene Function. PLoS Biol 6(7): e
18 Gene Wiki: features and contents o Contributions to Wikipedia as a specialized sub-section o Aims: provide a quality article for every notable human gene in the most used on-line encyclopedia o Some figures: o pages, visited millions of times o 86% of pages show up on the first page of Google (search by gene symbol) o 15,255 edits by 3,590 unique users in 2008 o Average increase of 236 kb of text per month (27 research letters in Nature) 18
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24 WikiGenes: References o WikiGenes o Hoffmann R: A wiki for the life sciences where authorsh 24
25 WikiGenes: features o Implements strict management of contributions authorship o Even small changes (single words) are assigned to an author o A web exist for each user, listing expertise, publications, and contributions o Authors can thus be evaluated and rated by peers o Includes a friendly editor, allowing for additions of specialized links 25
26 WikiGenes: editor setup o Chemical: allows annotation of terms as chemical compounds. Facilitates internal navigation and link to NCBI PubChem. o Gene: allows annotation of terms as genes. Enables users to internal navigation and link to NCBI Gene, Uniprot, SNPedia, o MeSH: alows annotation of terms as MeSH terms. Facilitates unambiguous internal navigation. o Reference: allows annotations of papers. Facilitates citation of articles listed in Pubmed. o Link: allows annotation of links to other pages. Enables linking of terms with articles in WikiGenes. o External link: allows annotation of terms with URLs. Enables linking to external web sites. 26
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38 WikiGenes: the movie Enjoy a movie now 38
39 ArrayWiki: References o ArrayWiki o Stokes TH, Torrance JT, Li H, Wang MD: ArrayWiki : an enabling technology for sharing public m 39
40 ArrayWiki: features An "intelligent" microarray repository that enables update of meta-data with the raw array data, and provides standardized archiving protocols o provides a user-friendly knowledge management interface (MediaWiki) o provides a user-curation capability through the familiar Wiki interface o provides text-based searches across experiment meta-data and exposes data to search engine crawlers o includes automated quality control processes (cacorrect) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality 40
41 ArrayWiki: statistics Unites meta-data from multiple sources, with following features: o provides a user-friendly knowledge management interface (MediaWiki) o provides a user-curation capability through the familiar Wiki interface o provides text-based searches across experiment meta-data and exposes data to search engine crawlers o includes automated quality control processes (cacorrect) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality 41
42 ArrayWiki: statistics Unites meta-data from multiple sources, with following features: 42
43 WikiPathways: References o WikiPathways o Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, et al. (2008) WikiPathways: Pathway Editing for the People. PLoS Biol 6(7): e bio
44 WikiPathways: features o A new model for pathway databases that enhances and complements ongoing efforts (KEGG, Reactome, Pathway Commons) o Peer review, editorial curation, and maintenance assigned to the community o Based on MediaWiki o Additionally: o a graphical pathway editing tool o integrated databases (major gene, protein, and small-molecule systems) 44
45 WikiPathways: interacting with pathways o One page per pathway, including: diagram, description, references, download options, version history, components o Pathways can be edited (embedded pathway editor) o History of changes and list of component are included with links to external resources o Users can monitor and undo changes o Pathways can be searched by name, included genes and proteins, text in descriptions and comments. o Pathways can be browsed by species names and by categories (ontology-based). o Pathways can be downloaded in many formats, including GPML 45
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53 WikiProteins: references o WikiProteins o Mons B, Ashburner M, Chichester C, et al., Calling on a million minds for comm WikiProteins, Genome Biology 2008, 9:R
54 WikiProteins: the concept space o Based on millions of biological concepts derived from UMLS, UniProtKB, IntAct, GO o Implements the original knowlet technology to store biological concepts and their relationships in the concept space o Proper filters allow to show sub-sections (semantic groups) as well as different types of relationships among concepts (strong only, all) o The concept space can be converted into RDF/OWL and searched by SPARQL 54
55 WikiProteins: wiki system o Unique wiki page per concept with data derived from the concept space o Concepts are identified on-the-fly and highlighted in the text o Navigation is allowed through internal (concepts-based) and external links o Registered users are allowed to edit wiki pages o Changes to data are evaluated and can be incorporated into databases 55
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