Plant Metabolic Pathways in MetaCyc and SolCyc
Correspondence: (Login to view email address)
- Boyce Thompson Institute, Cornell University
- SRI International, CA
- Boyce Thompson Institute
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- Document Type:
- Poster
- Date:
- Received 28 April 2009 12:38 UTC; Posted 28 April 2009
- Subjects:
- Bioinformatics
- Abstract:
MetaCyc is a metabolic encyclopedia of experimentally validated biochemical pathways curated from scientific literature, that spans all organisms, with an emphasis on plants and microbes. The Pathway tools is a complex curation software suite that enables curation of reactions, construction of pathways and annotation with one or more representative enzymes, that include information such as substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements, genes if cloned and links to external databases. In addition curators are able to provide concise, review-level summaries and extensive literature citations. The present database release includes more than 1200 pathways from more than 1549 organisms, 7312 reactions, 5127 enzymes, 4748 genes, 7234 chemical compounds, curated from 17916 citations. The MetaCyc database is the reference database on which the pathways are predicted from annotated genomes by PathoLogic called Pathway/genome Databases (PGDB’s). The Biocyc Database (biocyc.org) has a collection over 300 PGDB’s. Each BioCyc Database describes the genome and predicted metabolic pathways of a single organism, which are then taken up by interested groups for curation. SolCyc is one such PGDB, developed for the clade oriented Solanceae Genomics Network (SGN) database. It has predicted metabolic pathway databases of significant species belonging to Solanaceae and includes Lycocyc(tomato), Solacyc (eggplant), Nicotianacyc (tobacco),Petuniacyc (Petunia), Capcyc (Capsicum) , Potatocyc (potato). An interactive webinterface has been developed for the seamless flow of information from the SGN phenotype and locus database with SolCyc. This facilitates researchers with the capacity to search for underlying metabolic pathway information of genes and phenotypes that has been curated into the SolCyc database.
- Collection:
- 3rd International Biocuration Conference
- Presented at:
- 3rd International Biocuration Conference, 16 April 2009
Discussion
- Votes:
-
6 votes
- Comments:
-
2 comments
Hi Dan,
Most of the data in MetaCyc originates from dedicated curators, rather than from users contributions.
The majority of the data and associated citation entries were done by less than 12 curators over a period of 8-10 years.
There are many reasons why a particular entry (either a pathway or a protein) may have many citations. Two important reasons are 1. how important the topic is considered (the more important something is, the more publications are available about it) and 2. How thorough the curator is.
If a paper describes a large amount of work, detailing many enzymes involved in a pathway, then that paper will be cited for all the enzymes of that pathway, a well as the pathway itself. On the other hand a single reaction with a number of enzymes characterized from different organisms will carry many references.
Data can be submitted to SGN (gene and associated paper) by users having a login account to enter the data in the locus detail page using the community curation tools. If the gene is involved in a pathway, a nightly cron job associates the reaction to the gene. Clicking on the reaction on the SGN locus page will lead the users to the solcyc database. Additional curation at the Solcyc end is done by the SGN curators as it does not have community curation tools.
Hope this information helps
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Additional information
- License:
- This document is licensed to the public under the Creative Commons Attribution 3.0 License
- How to cite this document:
-
Pujar, Anuradha, Caspi, Ron, Menda, Naama, Tecle, Isaak, Karp, Peter, and Mueller, Lukas. Plant Metabolic Pathways in MetaCyc and SolCyc. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3192.1> (2009)
- Version info:
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Other versions of this document in Nature Precedings
None.
Other versions of this document elsewhere on the web
None known.
Dan Bolser on 09 June 2009 16:24 UTC
This work sounds really great! The 17k citations is really impressive! Can you provide a breakdown on this figure? i.e. how many annotators have provided these 17k citations? What is the distribution of annotators like? i.e. do you have some ‘super users’ who provided the bulk of the annotation and a ‘heavy tail’ of one-off annotators?
Similarly, how do the annotations break down per reaction? Which reaction has the most annotations (how many and how come) and which citation has gives the most reactions (how many and how come)?
How can I contribute information to SGN such that I can ‘seamlessly flow’ into SolCyc?