An exploration tool of Arabidopsis metabolism

ChloroKB

  1. Which browsers are compatible with ChloroKB?

    2. ChloroKB has been extensively tested using Google Chrome and Safari. Tests on IE10 and Firefox39 indicate that browsing is possible but that some functionalities will not work. We therefore recommend that you use Chrome. Do not forget to clear browsing data (cached images and files) to see modifications on maps and refresh the page(s).


  2. How do I cite ChloroKB?Top ↑

    3. "ChloroKB: a web-application for the integration of knowledge related to chloroplast metabolic network". Pauline Gloaguen P., Bournais S., Alban C., Ravanel S., Seigneurin-Berny D., Matringe M., Tardif M., Kuntz M., Ferro M., Bruley C., Rolland N., Vandenbrouck Y., Curien G. Plant Physiol. 2017 Jun;174(2):922-934


  3. Who can use ChloroKB?Top ↑

    4. Anyone can use ChloroKB! But it will be particularly useful for the following categories of scientists.

    • Biochemists, cell biologists and evolutionary biologists:

      • ChloroKB can help researchers to rapidly obtain up-to-date contextual information related to their protein(s) of interest (subcellular localization, position in the network, association in complexes, cofactors, detection in leaf). Evolutionary biologists will find a reference network for comparison with other plants or plant ancestors.

    • Modellers:

      • ChloroKB is intended to facilitate the process of model building (flux balance analysis, dynamic modelling). ChloroKB also compiles a wide-ranging selection of papers - not only from Arabidopsis - reporting kinetic parameters and metabolite abundance. This information should simplify the collection of quantitative information for model parametrization. For instance, it allows stoichiometry matrices to be built with high confidence.

    • Synthetic biologists:

      • ChloroKB will be very useful when grafting a pathway onto an existing network, thanks to the curated knowledge available for the pathway of interest, especially in terms of process compartmentalization and unforeseen connections. For instance it is far from trivial for a non-expert to know that L-cysteine degradation in the mitochondrion can generate L-asparagine in the cytosol; that alanine can be formed in the chloroplast as part of iron-sulfur formation; or that lumazine synthase, involved in riboflavin synthesis, is a 60-mer protein.

    • Research communication and training:

      • ChloroKB’s intuitive graphical representation can be used for research communication to share public information, propose/exclude hypotheses on solid grounds, avoid misunderstanding, correct errors, and improve knowledge.

      ChloroKB can be used for teaching purposes (teachers can gather information or find examples; students can rapidly assimilate knowledge accumulated over several decades of research on their subjects).

      ChloroKB can be used by experts in a field as a resource gathering recently-published information and to make their own work more visible.


  4. How do I search for my favorite protein?Top ↑

    5. ChloroKB’s search engine can be used either based on partial text matching or exact matching. From the search page (accessed through the "search ChloroKB tab" from the Home page) users may enter:

    • A full term between double quotes (e.g. "pyruvate kinase") to perform an exact search.
    • Part of a word without quotes (e.g. dehydro)
    • A protein name (e.g. synthase), a gene identifier (e.g. AT2G22250), a SwissProt accession number (e.g. P25851), part of a word (e.g. synth), a synonym or short names (e.g. OAS, OASTL, OAS-TL, Fd-GOGAT-2).
    • Searches can also be performed using multiple words or multiple AGIs (separated by a space: AT5G13280 AT5G14060 AT3G02020 AT1G31230 AT4G19710). In this case, the result of the search will be the sum of each single search.

    Query results will be displayed in two tabs: maps and molecules. Results are ranked according to a score corresponding to their relevance to the query (sorted in descending order). Briefly, this score is calculated based on the amount of information matched by attributing a weight to each field in the data model (document-oriented), and summing all weights to determine a cumulative score for a given term (present in a given field).


  5. Why is my favorite protein not in this database?Top ↑

    6. If a search for your favorite protein returns no results, it means that it has not yet been included in ChloroKB (e.g. it is still under review) or that it is not related to metabolism. Please contact the ChloroKB curators (mailto: chlorokb@cea.fr) for further information.


  6. Who do I contact if I find an annotation error?Top ↑

    7. If you notice an error or an omission, we would be very grateful if you could bring it to our attention for correction. To do this, please send an e-mail to ChloroKB (chlorokb) giving a precise description of the error/omission along with any public information available (e.g. author/year/paper or PMID); if your correction is based on unpublished data we will include the researcher's name and the information provided as a "personal communication" only after approval from the author.

    Please note that ChloroKB is centered on protein function. Selected references provide information on the molecular entities and their in vitro/in vivo function (KO analyses, downregulation, biochemical data and subcellular localization) or quantitative data on metabolites, proteins. Thus, the leading criterion for selection can be summarized by the following questions: Was the information present in the paper used to build the metabolic map? and, would the information be useful for modelling (FBA, kinetic modelling)? Papers that do not provide this kind of information have not been referenced.


  7. How to read a map (to which biological entities the color code of graphical object refers to)?Top ↑

    8. Detailed information associated with each graphical object can be found by clicking on the "Legend" ()button (located in the upper right part of each map).


  8. What does a hub metabolite map refer to?Top ↑

    9. A "hub" is a map representing highly connected metabolites (i.e., metabolites formed and consumed by several reactions). Thus, a "hub" map offers a different representation of metabolic pathways centered on a hub metabolite (e.g. pyruvate, L-aspartate,) or on several highly-connected metabolites (e.g. G3P_DAHP_PEP_E4P_HUB, Glucose 1-phosphate and Glucose 6-phosphate). All known inputs and outputs are represented along with the enzymes involved. Note that the information contained in hub maps is also present in other maps


  9. How the status (reviewed/unreviewed) is assigned to a map?Top ↑

    10. Maps included in ChloroKB were labeled with a status (“reviewed” or “unreviewed”) to indicate whether they have been revised by at least one independent expert (not involved in the map-building stage); an “unreviewed” status indicates that the map is currently undergoing revision.


  10. How the status (reviewed/unreviewed) is assigned to a protein?Top ↑

    11. Information for a given protein is considered as reviewed when the literature on the protein has been carefully examined, the relevant references selected, the localization curated and the reaction field completed. Information for unreviewed proteins may have been automatically extracted and/or not checked at all, or only partially reviewed.


  11. How the field “Curated localization” is annotated (in relationship with “Localization evidence”)?Top ↑

    12. The field “curated localization” (e.g. plastid, chloroplast, mitochondrion, stroma, etc.) contains information relating to the evidence presented in the “localization comment” field. This evidence includes the features of the protein (e.g. presence or absence of N-terminal extension) and the type of experimental data (western blots, proteomics data, activity measurements, etc.) which has been used to establish the curated localization status of the protein. The corresponding references are indicated in the localization comment field. This field also contains information about the experimental detection of the protein in leaf (the reference tissue in ChloroKB).


  12. What cross-references were considered for the metabolite records?Top ↑
    13. MetaCyc Metacyc accession ; reference database for update
    CAS identifier for Chemical Abstract Services
    ChEBI identifier in the ChEBI resource
    KEGG identifier in the KEGG database (compound section)
    PubChem Compound CID + chemical structure

    The different accession identifiers are used to crossreference ChloroKB to these popular databases. The description page for the different metabolites shows a chemical structure extracted from PubChem Compound. N.B. when no PubChem Compound identifier is available for a metabolite, no chemical structure can be displayed.