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DOQCS Help


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Last updated: February 24, 2005


DOQCS Searches

 

DOQCS Searches

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  The Database of Quantitative Cellular Signaling (DOQCS) was developed at the National Centre for Biological Sciences (NCBS), Bangalore, India. The FAQ contains additional information.

  Searching DOQCS is easy: just enter search terms in the query box and press the Enter key or click Submit. The brown coloured Search Bar provides access to additional search options. The DOQCS query box and Search bar are available from every screen, so you don't need to return to the homepage to enter a new search.

  You may enter one or more terms (e.g. Ca IP3 CaM) in the query box and DOQCS automatically combines (ANDs) terms together. The terms are searched in various table entries. Once you click Submit, DOQCS will display your search results. The query box displays your search terms as you entered them. You can modify your current search by adding or eliminating terms in the query box.
 

Search Rules

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  • Boolean  

    • Only AND Boolean operator is allowed on DOQCS.

    • When combining query terms either AND or a blank space can be used to separate the multiple query terms.

    • Usage of AND is case insensitive, e.g. Ca AND IP3 AND CaM yields the same result as Ca and IP3 and CaM.



  • Search Field Qualification 

      Query terms can be qualified using DOQCS' Search Tags.

    • Add the search tag after the term, e.g., CaMKII[mol].

    • Search field tags must be enclosed in square brackets, [mol].

    • Neither case nor spacing of the search tags matter, e.g., CaMKII [mol] = CaMKII[mol].

    • The order of the search tags too is unimportant, e.g., CaMKII[mol][e][na] = CaMKII[e][na][mol].



  • Search Tags 

      Query terms on DOQCS can be qualified using case insensitive search tags for different Search Fields, Match Fields and Match Types. Though search tags can be used together from all the three field qualifiers, only one search tag of a particular qualifier can be used at a time. If more than one search tag of a qualifier is used then results are returned based on the last tag entered.

     E.g. A search like CamKII[PATH][E][NA][MOL] translates into a search for the exact term CaMKII in the name field for both pathway and molecule. The syntax for this search is incorrect because it uses [PATH] and [MOL] both of which are tags for the Search Field together for a single query term. Thus the first tag is ignored and DOQCS returns the results for exact matches of CaMKII in the name field of molecule table.

      Search Field Qualifiers:

    • All Search Fields [ALL] Used, to search in DOQCS across all tables.

    • Accession [ACC] Used, to search only in DOQCS Accession tables, for full models.

    • Pathway [PATH] Used, to search only in DOQCS Pathway listings.

    • Molecule [MOL] Used, to search in Molecule table of DOQCS.

    • Enzyme [ENZ] Used, to search DOQCS only in Enzyme table.

    • Reaction [REA] Used, to search in Reaction table of DOQCS.

    • Connected to [CT] Used, to search the distribution of the query term across different table entries.


      Match Field Qualifiers

    • Anything [A] Used, to search for the query term found anywhere within the string.

    • Exact Word [E] Used, to run a search for the exact word.

    • Starting With [S] Used, to search for all terms that begin with the query term.


      Match Type Qualifiers

    • Name [NA] Used, to do a wild card search in DOQCS across all tables.

    • Notes [E] Used, to run a search for the exact word.


 

SearchBar

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  The brown coloured Search bar on top of a DOQCS page provides access to additional search options. Use of the relevant options allows to limit your retrieval to a specific subset of tables within DOQCS, such as search for MAPK entries only within reactions or enzymes.

Search Field

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  • ALL  

      To search all table entries on DOQCS, enter search terms in the query box and press the Enter key or click Submit. Default searches on DOQCS are done in All Tables and the results are not exact word matches; e.g querying for PKC will yield degraded-PKC, PKC and PKC-active among the search results. All results here will have PKC but it is not an exact word match.

     To get an exact word match select "Exact Word" from the Match Field and then query for the search term. The same result can be got by qualifying the querying term using Search Tags as follows PKC[e] or PKC[E].


  • Accession 

      To search all accession names on DOQCS, enter search terms in the query box; now, from the drop down menu of the search field select Accession and press the Enter key or click Submit. An accession name is essentially the name of a model on DOQCS. Default accession searches on DOQCS are done in the name field and the results are not exact word matches; e.g querying for CaMKII in accession list will yield fig3_CaMKII, CaMKII and CaMKII_2003 among the search results. These are three models that have CaMKII in their accession names. But these are not the only models on DOQCS that have CaMKII as participating molecules.

      E.g. Osc_Ca_IP3metabolism is a model on DOQCS that has CaMKII as one of its participating molecules. But this is not returned as a result for CaMKII accession search because the model name is "Osc_Ca_IP3metabolism" and does not have CaMKII in its name. To search for all accessions that have CaMKII as a participating molecule check the Model results in Connected to table.


  • Pathway 

      To search all pathway names on DOQCS, enter search terms in the query box; now, from the drop down menu of the search field select Pathway and press the Enter key or click Submit. A pathway is not always synonymous to an accession or a model; by itself a pathway means a sequence of biochemical reactions. An accession name can be of either a pathway model or a network model. Networks are a collection of interconnected pathways that together form a network model. E.g. egfr signaling pathway is an example of a pathway on DOQCS that is a model in itself and therefore has an accession name. EGFR_MAPK is an example of a network on DOQCS that is a model in itself and therefore has an accession name. This network is composed of MAPK, Ras, EGFR and Sos pathways.

      Default pathway searches on DOQCS are done in the name field and the results are not exact word matches. E.g. querying for CheY in the pathway list may not yield any results. But this does not mean that there are no models on DOQCS that have CheY as participating molecules.

     There are pathways named Chemotaxis on DOQCS that has CheY as one of its participating molecules. But this is not returned as a result for CheY pathway search because the model name is "Chemotaxis" and does not have CheY in its name. To search for all pathways that have CheY as a participating molecule check the Model results in Connected to table.


    Shared Object  

      The Shared_Object_pathway is the collection of molecules, enzymes and reactions that occur in more than one pathway within a network model. These are responsible for communication between the pathways in the network. Some molecules, enzymes and reactions shown in the reaction scheme diagram for a pathway in older network models, might not be listed in the respective lists for the pathway. These are probably a part of the Shared Object and would be listed under Shared_Object_pathway.

     E.g. the molecules cAMP, GTP.Ga and PKA-active are shared molecules in the PKA_2003 model and are listed under pathway name Shared_Object_PKA_2003

      This rather clumsy approach will be replaced within kinetikit with the evolution of the object-oriented pathway definitions in kinetikit 8 and later, which utilize the concept of interaction interfaces to communicate between pathways. Older network models which use the Shared_Object_pathway will continue to be represented in their original form.


  • Molecule  

      To search all molecule names on DOQCS, enter search terms in the query box; now, from the drop down menu of the search field select Molecule and press the Enter key or click Submit. Default molecule searches on DOQCS are done in the name field and the results are not exact word matches; e.g querying for CaM in the molecule list will yield results not just for CaM but also for CaMKII, 3kCam*_ip3_cmplx, AC1-CaM. To get an exact word match for CaM in molecule list select "Exact Word"; from the Match Field and then query for the search term. The same result can be got by qualifying the querying term using Search Tags as follows CaM[e][mol] or CaM[E][MOL].


  • Enzyme  

      The notation for enzymes on DOQCS is Enzyme Molecule/Enzyme activity. The same molecule can have various enzymatic activities. E.g. PKC-active is an enzyme in the fig2_egfr network model that has three different enzymatic activities in the model viz. PKC-active/PKC-act-raf, PKC-active/PKC-inact-GAP and PKC-active/PKC-act-GEF.

      To search all enzyme names on DOQCS, enter search terms in the query box; now, from the drop down menu of the search field select Enzyme and press the Enter key or click Submit. Default enzyme searches on DOQCS are done in the name field of both the molecule and the enzyme activity and the results are not exact word matches; e.g querying for GAP in the enzyme list will yield results not just for GAP but also for PKC-active/PKC-inact-GAP among others. To get an exact word match for GAP in the enzyme list select "Exact Word" from the Match Field and then query for the search term. The same result can be got by qualifying the querying term using Search Tags as follows GAP[e][enz] or GAP[E][ENZ].


  • Reaction  

      To search all reaction names on DOQCS, enter search terms in the query box; now, from the drop down menu of the search field select Reaction and press the Enter key or click Submit. Default reaction searches on DOQCS are done in the name field and the results are not exact word matches; e.g querying for CaM in the reaction list will yield results not just for CaM but also for CaMKII. To get an exact word match for CaM in reaction list select "Exact Word" from the Match Field and then query for the search term. The same result can be got by qualifying the querying term using Search Tags as follows CaM[e][rea] or CaM[E][REA].


  • Connected to  

      The Connected to search feature on DOQCS, is an easy way to find out how the query term is related to different table entries viz.Accession (Model), Pathway, Molecule, Enzyme and Reactions E.g. Searching for MAPK on DOQCS shows many results in molecule list. But if you are interested only in those reactions in which MAPK is a substrate those results can be obtained from the Connected to results.

      To search distribution of query term across all tables in DOQCS enter the terms in the query box; now, from the drop down menu of the search field select Connected to and press the Enter key or click Submit. Default connected to searches on DOQCS are done in the name field and the results are not exact word matches; e.g querying for CaM in the connected to list will yield results not just for CaM but also for CaMKII. To get an exact word match for CaM in reaction list select "Exact Word"; from the Match Field and then query for the search term. The same result can be got by qualifying the querying term using Search Tags as follows CaM[e][ct] or CaM[E][CT].


 

Match Field

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  • Anything  

      Default DOQCS search looks for the query term anywhere in the string. When the Match field parameter Anything is selected from the drop down menu or when default searches are run, DOQCS is queried for any form of occurrence of the query term. E.g. When DOQCS is searched for Ca the actual search is done for wild card Ca wild card and this will yield AC1-CaM, Ca and CaMKII in the search results.

  • Exact Word  

      When the Match field parameter Exact Word is selected from the drop down menu and the searches are run, DOQCS is queried for the occurrence of the exact query term. E.g. When an Exact Word search is executed for Ca, the actual search is done exactly for Ca and this will yield only Ca in the search results and not AC1-CaM or CaMKII.

  • Starting With  

      When the Match field parameter Staring With is selected from the drop down menu and searches are run, DOQCS is queried for occurrences of all terms that begin with the query term. E.g. When a Starting With search is executed for Ca the actual search is done for Ca wild card and this will yield Ca and CaMKII among the search results, but not AC1- CaM.


Match Type

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  • Name  

      In the default DOQCS searches the query term is matched against the names for different entries of the tables. The names of the table entries are the identifying tags for each entry.


  • Notes 

      When the Match type parameter Notes is selected from the drop down menu and the searches are run, DOQCS is queried for the occurrence of the query term in the notes (if any) for each table entry. This feature could be used for searching for citations on DOQCS. E.g. When a Notes search is executed for Kholodenko the search results yield in Accession MAPK models originally developed by Kholodenko.

      Currently exact word and starting with searches for two search term is not allowed in the Notes field. Since the search is done in notes field if DOQCS is searched for Ca in notes field in addition to results such as NonOsc_Ca_IP3metabolism and PKC-Ca-AA* english words like "can", cascade etc. will also end up in the search results.


  • Model 

      When the Match type parameter Model is selected from the drop down menu and the searches are run, DOQCS is queried for Accession (Model) or Pathway in the Molecule table entry. This feature could be used for searching Model in which the query term is present as a molecule on DOQCS. E.g. When a Model search is executed for Ca and IP3 the search results yield in Accession And Pathway in which both Ca and IP3 are present individual or together.
    For an e.g in Accession list "NonOsc_Ca_IP3metabolism" is displayed because it has IP3_3K_CaM* in Molecule table and "fig2_egfr" is displayed because it has Ca and IP3


 

Links

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  • PubMed Abstarcts  

      Many table entries on DOQCS have citations in the notes. Whenever the citations are articles they are linked out to the abstract if available on NCBI PubMed.


  • Demo Simulations  

      Many accession entries on DOQCS are based on in-house publications. Some of these publications have demo simulations available. These demo simulations are available through appropriate links from the accession notes.


Citation

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  The citation for DOQCS is

    Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US.
    "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks."
    Bioinformatics. 2003 Feb 12;19(3):408-15.



DOQCS Team




Database compilation and code copyright (C) 2005, Upinder S. Bhalla and NCBS/TIFR
This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details.