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Mediawiki Manual

Ver 1.14

 

GENERAL HELP 
 

Steps to create a new page on Mediawiki : 


1. Open new web page and in the browser type the URL  http://hubtb.osdd.net/mediawiki/.


2. You will see the main page having list of RvIDs.Just click on the specific ID and you will be directed to that page.



    image

    3. Then you will be able to see an empty wiki page( as shown below), click on the edit tab. 

    image 

     4. Copy & paste the code highlighted in yellow (given at the end of steps with respective page name) in the text area of the edit box



    image  
    5.    Then click on the save page button to save the changes you made in the edit box.

    6.    After saving this page you will be directed back to the Rv ID page from where you started and you will notice 2 things on the page[i.e. 6(a)& 6(b)]:


      6(a) The tabs created at the top of the page are in blue bar format within which the links colured in red are the pages which still donot exist. Once you click on them you will be directed to a newpage (for example to page 2 i.e. Gene). 

      This is how the first page will be completed, you need to follow the above 1-5(a) steps, to complete the eight set of pages.After you have created the last page (i.e References) come back to the first page by clicking on the Quickview tab.

      The 8 set of pages

      Page1:Rv ID:Quickview

      Page2:Rv ID :Gene

      Page3:Rv ID:Gene Product(s)

      Page4:Rv ID:Expression

      Page5:Rv ID:Evolution

      Page6:Rv ID:Pathway Information

      Page7:Rv ID:MTb Localizations

      Page8:Rv ID:References

       

      6(b) The second thing will be an empty table created on the second half of the page.You need to click on the edit table link and follow the steps shown below with screenshots in the heading called “HOW TO EDIT TABLE IN A PAGE”. 
       
       

      THE CODES WHICH NEED TO BE COPIED ON RESPECTIVE PAGES (Step:4) 


      Page1 - Rv ID:Quickview


      {|style="background:#99BADD; color:white" border="2" cellpadding="7" cellspacing="2"

      | Quickview

      |[[RvID:Gene |Gene]]

      |[[RvID:Gene Product(s) |Gene Product(s)]]

      |[[RvID:Expression |Expression]]

      |[[RvID:Evolution |Evolution]]

      |[[RvID:Pathway Information |Pathway Information]]

      |[[RvID:MTb Localizations | MTb Localizations]]

      |[[RvID:References | References]]

      |} 

      == Quickview ==

      <newTableEdit>Standard Name 
      Gene Synonym(s)  
      Product Synonyms(s)

      Knock-Out Phenotype 
      Regulation/Expression

      Regulation/Activity

      </newTableEdit> 

      '''Notes'''

      {{BacktoTop}} 
       
       

      Page2 - Rv ID:Gene 


      {|style="background:#99BADD; color:white" border="2" cellpadding="7" cellspacing="2"

      |[[RvID| Quickview]]

      |[[RvID:Gene |Gene]]

      |[[RvID:Gene Product(s) |Gene Product(s)]]

      |[[RvID:Expression |Expression]]

      |[[RvID:Evolution |Evolution]]

      |[[RvID:Pathway Information |Pathway Information]]

      |[[RvID:MTb Localizations | MTb Localizations]]

      |[[RvID:References | References]]

      |}

      {|

      |- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"

      |{{Sub}}[[#Nomenclature |Nomenclature]]

      |{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]

      |{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]

      |{{Sub}}[[#Genetic Resources  |Genetic Resources]]

      |{{Sub}}[[#Accessions in Other Databases |Accessions]]

      |{{Sub}}[[#Links |Links]]

      |} 

      == Nomenclature ==

      <newTableEdit>Standard name 
      Mnemonic  
      Synonyms  
      </newTableEdit>       
       

      == Location(s) and DNA Sequence ==

      {{BacktoTop}}

      <newTableEdit>Strain  
      Map location 
      Genome coordinates 
      Genome browsers

      Sequence links

      </newTableEdit> 

      == Sequence Features ==

      {{BacktoTop}}

      <newTableEdit>Feature type 
      Location 
      Description  
      </newTableEdit>       

      == Alleles and Phenotypes ==

      {{BacktoTop}}

      <newTableEdit>Allele 
      Nt change(s) 
      AA change(s) 
      Phenotype: Description

      Reference

      Availability

      Comments

      </newTableEdit> 

      == Genetic Resources ==

      {{BacktoTop}}

      <newTableEdit>Resource 
      Resource Type

      Source 
      Notes/Reference</newTableEdit>       
       

      == Accessions in Other Databases ==

      {{BacktoTop}}

      <newTableEdit>Database 
      Accession 
      Notes 
      </newTableEdit>       
       

      == Gene Information ==

      {{BacktoTop}}

      <newTableEdit>GeneName  
      GeneSymbol

      GenomicLocation  
      LocusId

      GeneIdEntrez
      GeneIdGenbank 
      OrfFunctionP  
      GeneOntologyIdBp  
      GeneOntologyIdMf  
      GeneOntologyIdCc  
      CodonAdaptationIndex  
      OrthologGeneId

      CogAnnotation

      CogGeneName  
      CogId  
      OperonSharedGenes  
      OperonSharedGenes  
      EssentialGenesSassettietal  
      EssentialityInformation  
      EssentialityInformationP  
      GeneDuplicationClusterId 
      HorizontalTransferId  
      HorizontalTransferId  
      GeneSequence  
      Gene Resources Related Entries  
      Related References   
      Related Resources </newTableEdit>       

      == Protein Motif Information ==

      {{BacktoTop}}

      <newTableEdit>PrintsMotif  
      PrositeMotif  
      CopsPeptide  
      CopsFunctionObserved 
      CopsHomologyHuman  
      CopsMutationObserved  
      PfamDomainId

      SwissProtId
      RelatedReferences   
      RelatedResources  
      </newTableEdit>       

      == Links ==

      {{BacktoTop}}

      <newTableEdit>Name 
      URL

      Comments  
      </newTableEdit>

      __NOTOC__ 
       

      Page3 - RvID:Gene Product(s) 


      {|style="background:#99BADD; color:white" border="2" cellpadding="7" cellspacing="2"

      |[[RvID| Quickview]]

      |[[RvID:Gene |Gene]]

      |[[RvID:Gene Product(s) |Gene Product(s)]]

      |[[RvID:Expression |Expression]]

      |[[RvID:Evolution |Evolution]]

      |[[RvID:Pathway Information |Pathway Information]]

      |[[RvID:MTb Localizations | MTb Localizations]]

      |[[RvID:References | References]]

      |}

      {|

      |-

      |{{Sub}}[[#Nomenclature |Nomenclature]]

      |{{Sub}}[[#Function |Function]]

      |{{Sub}}[[#Interactions |Interactions]]

      |{{Sub}}[[#Localization |Localization]]

      |{{Sub}}[[#Sequence|Sequence]]

      |{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]

      |{{Sub}}[[#Structure|Structure]]

      |{{Sub}}[[#Gene Product Resources|Resources]]

      |{{Sub}}[[#Accessions in Other Databases |Accessions]]

      |{{Sub}}[[#Links |Links]]

      |} 
       

      ==Nomenclature==

      <newTableEdit>Standard name 
      Synonyms  
      Product description  
      EC number (for enzymes)

      </newTableEdit> 
       

      ==Function==

      {{BacktoTop}} 

      '''Gene Ontology''' 

      '''DNA polymerase III''' 

      <newTableEdit>Qualifier 
      GO ID  
      GO term name 
      Reference(s)  

      Evidence Code

      with/from 

      Aspect  

      Notes

      Status </newTableEdit> 

      '''Interactions''' 

      '''DNA polymerase III'''

      <newTableEdit>Partner Type 
      Partner  
      Notes 
      References 
      Evidence  
      </newTableEdit>       

      ==Localization==

      {{BacktoTop}}

      <newTableEdit>

      Compartment  
      Description  
      Evidence  
      Notes  
      </newTableEdit>       
       

      ==Structure and Physical Properties==

      {{BacktoTop}}

      '''Physical Properties'''

      <newTableEdit>Sequence  
      Length  
      Mol. Wt  
      pI  
      Extinction coefficient 
      </newTableEdit>       
       

      '''Domains/Motifs/Modification Sites''' 

      <newTableEdit>Type 
      Residues 
      Description  
      Notes</newTableEdit>       

      '''Structure'''

      <newTableEdit>Struture 
      Models  
      </newTableEdit>       
       

      == Gene Product Resources ==

      {{BacktoTop}}

      <newTableEdit>Resource Type 
      Source   
      Notes/Reference 
      </newTableEdit>       

      ==Accessions in Other Databases==

      {{BacktoTop}}

      <newTableEdit>Database 
      Accession  
      Notes  
      </newTableEdit>       

      ==Links==

      {{BacktoTop}}

      <newTableEdit>Name 
      URl  
      Comments 
      </newTableEdit>       

      __NOTOC__ 
       
       
      Page4 - RvID:Expression 

       

      {|style="background:#99BADD; color:white" border="2" cellpadding="7" cellspacing="2"

      |[[RvID| Quickview]]

      |[[RvID:Gene |Gene]]

      |[[RvID:Gene Product(s) |Gene Product(s)]]

      |[[RvID:Expression |Expression]]

      |[[RvID:Evolution |Evolution]]

      |[[RvID:Pathway Information |Pathway Information]]

      |[[RvID:MTb Localizations | MTb Localizations]]

      |[[RvID:References | References]]

      |}

      {|

      |-

      |{{Sub}}[[#Overview|Overview]]

      |{{Sub}}[[#Transcription and Transcriptional Regulation|Transcription]]

      |{{Sub}}[[#Translation and Regulation of Translation|Translation]]

      |{{Sub}}[[#Turnover and Regulation of Turnover|Turnover]]

      |{{Sub}}[[#Experimental|Experimental]]

      |{{Sub}}[[#Links| Links]]

      |} 

      == Overview ==

      t

      e

      x

      t 

      ==Intracellular Levels==

      {{BacktoTop}}

      <newTableEdit>Molecule  
      Organism or Strain 
      Molecules per cell 
      Growth conditions 
      Growth rate 
      Assay used 
      Notes 
      Reference(s)

      </newTableEdit>

      '''Notes''' 

      ==Transcription and Transcriptional Regulation==

      {{BacktoTop}}

      <newTableEdit>Transcription unit(s) 
      FIGURE  
      </newTableEdit>       
       

      ==Translation and Regulation of Translation== 
       

      Figure

      __NOTOC__

      '''Notes''' 

      ==Turnover and Regulation of Turnover==

      {{BacktoTop}} 

      '''Notes''' 
       
       

      ==Experimental==

      '''Mutations Affecting Expression'''

      <newTableEdit>Allele Name 
      Mutation  
      Phenotype 
      Reference</newTableEdit>       
       

      '''Expression Studies'''

      <newTableEdit>Type 
      Reference 
      Notes</newTableEdit>       

      '''Expression Resources'''. 

      <newTableEdit>Resource Name

      Resource Type 
      Description 
      Source

      Notes</newTableEdit> 
       
       

      '''Notes''' 

      ==Accessions Related to its Expression==

      {{BacktoTop}}

      <newTableEdit>Database 
      Accession 
      Notes  
      </newTableEdit>

      '''Notes''' 

      ==Links==

      {{BacktoTop}}

      <newTableEdit>Name  
      URL 
      Comments 
      </newTableEdit>       
       

      __NOTOC__ 
       
       

      Page5 - RvID:Evolution 
       

      {|style="background:#99BADD; color:white" border="2" cellpadding="7" cellspacing="2"

      |[[RvID| Quickview]]

      |[[RvID:Gene |Gene]]

      |[[RvID:Gene Product(s) |Gene Product(s)]]

      |[[RvID:Expression |Expression]]

      |[[RvID:Evolution |Evolution]]

      |[[RvID:Pathway Information |Pathway Information]]

      |[[RvID:MTb Localizations | MTb Localizations]]

      |[[RvID:References | References]]

      |}

      {|

      |-

      |{{Sub}}[[#Homologs in Other Organisms|Homologs]]

      |{{Sub}}[[#Families|Families]]

      |{{Sub}}[[#Links| Links]]

      |{{Sub}}[[#References| References]]

      |} 

      == Homologs in Other Organisms ==

      {{BacktoTop}}

      <newTableEdit>Organism 
      Homologs (Statistics) 
      Comments  
      </newTableEdit>       
       

      '''Do-It-Yourself Web Tools'''

      *[http://130.14.29.110/BLAST/ BLAST]

      *[http://130.14.29.110/BLAST/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=250&ALIGNMENT_VIEW=Pairwise&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&CDD_SEARCH=on&DESCRIPTIONS=500&ENTREZ_QUERY=%28none%29&EXPECT=10&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on&SERVICE=plain&SET_DEFAULTS.x=36&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes&SEARCH_NAME=psi_bp/ CDD]

      *[http://inparanoid.sbc.su.se/cgi-bin/gene_search.cgi?id=&idtype=all&all_or_selection=all&specieslist=1&scorelimit=0.05&.submit=Submit&.cgifields=specieslist&.cgifields=idtype&.cgifields=all_or_selection InParanoid]

      *[http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/ YOGY] 
       

      '''Notes''' 

      == Families ==

      {{BacktoTop}}

      <newTableEdit>Database 
      Accession 
      Notes  
      </newTableEdit>       

      '''Notes''' 

      == Links ==

      {{BacktoTop}}

      <newTableEdit>Name 
      URI 
      Comments  
      </newTableEdit>       

      == References ==

      {{BacktoTop}} 

      '''Categories''' 

      __NOTOC__ 
       
       

      Page6 - RvID:Pathway Information 


      {|style="background:#99BADD; color:white" border="2" cellpadding="7" cellspacing="2"

      |[[RvID| Quickview]]

      |[[RvID:Gene |Gene]]

      |[[RvID:Gene Product(s) |Gene Product(s)]]

      |[[RvID:Expression |Expression]]

      |[[RvID:Evolution |Evolution]]

      |[[RvID:Pathway Information |Pathway Information]]

      |[[RvID:MTb Localizations | MTb Localizations]]

      |[[RvID:References | References]]

      |} 

      <newTableEdit>MetabolicReactionId  
      PathwayModelId 
      KeggPathwayId 
      KeggPathwayName 
      KeggPathwayProduct 
      KeggPathwaySubstrate 
      KeggReactionId 
      KeggReactionName  
      KeggReactionSubstrate 
      RelatedEntries 
      RelatedReferences  
      RelatedResource 
      </newTableEdit>

      {{BacktoTop}} 
       
       
       

      Page7 - RvID:MTb Localizations 


      {|style="background:#99BADD; color:white" border="2" cellpadding="7" cellspacing="2"

      |[[RvID| Quickview]]

      |[[RvID:Gene |Gene]]

      |[[RvID:Gene Product(s) |Gene Product(s)]]

      |[[RvID:Expression |Expression]]

      |[[RvID:Evolution |Evolution]]

      |[[RvID:Pathway Information |Pathway Information]]

      |[[RvID:MTb Localizations | MTb Localizations]]

      |[[RvID:References | References]]

      |}

      <newTableEdit>
      PajonetalOuterMembraneP 
      PajonetalBetabarrelLength  
      PsortProteinName     
      PsortGeneName     
      PsortE  
      PsortP  
      PsortScore  
      PsortDbversion
      PsortCmsvm  
      PsortCytosvm 
      PsortEcsvm 
      PsortHmmtop  
      </newTableEdit>
      <newTableEdit>
      PsortHmmtopHelicesCount
      PsortMotifLocalization  
      PsortMotifDetails  
      PsortOmpmotif  
      PsortOmpmotifDetails  
      PsortOmsvm  
      PsortPpsvm   
      PsortProfileLocalisation  
      PsortProfileDetails   
      PsortSclblast   
      PsortSclblastDetails   
      PsortSclblasteLocalisation
      </newTableEdit>
      <newTableEdit>  
      PsortSclblasteDetails  
      PsortSignalLocalisation 
      PsortSignalDetails  
      PsortSubloccLocalisation 
      PsortCellwallScore  
      PsortCytoplasmicScore 
      PsortCytoplasmicmembraneScore
      PsortPeriplasmicScore  
      PsortOutermembraneScore
      PsortExtracellularScore
      </newTableEdit>
      <newTableEdit>

      PslpredP

      SwissprotAnnotation
      TbpredP
      RelatedEntries 
      RelatedReferences 
      RelatedResources
      </newTableEdit>

      {{BacktoTop}} 

       

      Page8 - RvID:References 


      {|style="background:#99BADD; color:white" border="2" cellpadding="7" cellspacing="2"

      |[[RvID| Quickview]]

      |[[RvID:Gene |Gene]]

      |[[RvID:Gene Product(s) |Gene Product(s)]]

      |[[RvID:Expression |Expression]]

      |[[RvID:Evolution |Evolution]]

      |[[RvID:Pathway Information |Pathway Information]]

      |[[RvID:MTb Localizations | MTb Localizations]]

      |[[RvID:References | References]]

      |} 

      <newTableEdit>RelatedEntries  
      RelatedResources  
      RelatedReferences

      </newTableEdit>

      {{BacktoTop}} 
       

      NOTE:Do not forget to replace the RvID with the specific Rv id number on each page.For any formatting queries you may refer to Rv0721. 


      HOW TO EDIT TABLE IN A PAGE


      TableEdit provides a somewhat more friendly way to edit simple tables in mediawiki. TableEdit tables show up in a page with their own Edit link, which calls this page. Users who have editing privileges can then add rows and columns, rename headings, and change the style of the headings row.


      Step 1 : Click on the Edit Table link to go to the Table Edit special page (Figure 1) 


      Figure 1

        

      Step 2 : Click on Add Data to add data in another row. Click on Edit to add data in already created rows (Figure 2)


      image  
             Figure 2    

       
      Step 3 : Save the new row in the edit page. Note that it has not been saved back to the wiki page yet. To save in wiki page Click on save table to wiki. 

      image



       F      igure 3

       
       

      Step 4 : Make the heading background light pink by adding heading style (Figure 4) as {{table_heading_style}}

         

         

        image

        (Figure 4) 


        Step 5 : Save back to the editor again by clicking on Save Table to wiki page:RV ID

           

                                            


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