Dokuwiki for science

Bio plugin

:!: This plugin is deprecated :!:

This DokuWiki plugin provides some utilities for biology and biochemistry. This plugin is a sort of class library which does not extends DokuWiki_syntax_plugin. (2.8KB)2008-03-22


In order to define all classes, read 'bio.php'. This entry script will read all classes if they don't exist.


NCBI class

This class accesses to NCBI Entrez database.


eSummaryURLString format to retrieve XML file of database and ID
eSearchURL String format to search in NCBI database by terms
pubchemURL String format to retrieve XML file of PubChem
pubmedURL String format to make a link to PubMed


SummaryXml($db,$id)Retrieve a summary XML data of $db database by using unique ID from NCBI.
SearchXml($db,$terms) Get search result XML of terms from NCBI.
PDBtoStructureID($pdbAcc)Convert to PDB ID to NCBI Structure ID
GetPubchemXml($cid)Get a Pubchem summary XML data from NCBI.
GetSummaryItem($item,&$xml)Extract an item element from Summary XML
GetSummaryItems($item,&$xml)Extract some items from Summary XML
GetSearchItem($item,&$xml)Extract an item element from Search XML
GetSearchItem($item,&$xml)Extract some items from Search XML

RCSB class

This class accesses to RCSB PDB site.


ImgURL String format of URL to retrieve an image of PDB
LinkURL String format to make a link to a specific PDB
LinkFormatString format to make a link html of PDB Explorer


DownloadImage($pdbid,$path)Download an image to $path using PDB ID from RCSB site.
ExplorerURL($pdbid) Create a URL to a specific PDB entry.
ExplorerLink($pdbid) Create a link html to a specific PDB entry.
PDBformat($pdbid) Check PDB ID

XML class

This class is a simple class for XML parser.


tagTag name
valueElement value
attributesAttributes of this element
nextArray of child classes


  • 2008.3.22
    • First version was uploaded.