There are DokuWiki plugins for research & education which I developed. All plugins are under GPL2 license, so feel free to use them in your DokuWiki.
Dokuwiki Official
DokuWiki plugins for bioscience and biotechnology.
This wiki contains information about source codes for DokuWiki plugin.
This is a plugin for DokuWiki that retrieves the information from PubMed widh PMID. The plugin stores NCBI ESummary XML file in /data/media/ncbi_esummary directory.
{{pubmed>[Command]:[PubMed ID]}}
| Command | item | function |
|---|---|---|
| short | link | Show a short pubmed link from NCBI Structure database |
| long | link | Show a detailed pubmed link from NCBI Structure database |
| summaryXML | xml | Show a XML summary data from the NCBI database using Entrez Utilities |
| clear_summary | - | Clear cached XML files in /data/media/ncbi_esummary |
| remove_dir | - | Clear cached files and remove cache directory |
{{pubmed>short:9039911}}
{{pubmed>long:9039911}}
{{pubmed>summaryXML:9039911}}
<?xml version="1.0" encoding="UTF-8" ?> <!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary v1 20041029//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20041029/esummary-v1.dtd"> <eSummaryResult> <DocSum> <Id>9039911</Id> <Item Name="PubDate" Type="Date">1997 Feb 27</Item> <Item Name="EPubDate" Type="Date"></Item> <Item Name="Source" Type="String">Nature</Item> <Item Name="AuthorList" Type="List"> <Item Name="Author" Type="String">Wilmut I</Item> <Item Name="Author" Type="String">Schnieke AE</Item> <Item Name="Author" Type="String">McWhir J</Item> <Item Name="Author" Type="String">Kind AJ</Item> <Item Name="Author" Type="String">Campbell KH</Item> </Item> <Item Name="LastAuthor" Type="String">Campbell KH</Item> <Item Name="Title" Type="String">Viable offspring derived from fetal and adult mammalian cells.</Item> <Item Name="Volume" Type="String">385</Item> <Item Name="Issue" Type="String">6619</Item> <Item Name="Pages" Type="String">810-3</Item> <Item Name="LangList" Type="List"> <Item Name="Lang" Type="String">English</Item> </Item> <Item Name="NlmUniqueID" Type="String">0410462</Item> <Item Name="ISSN" Type="String">0028-0836</Item> <Item Name="ESSN" Type="String">1476-4687</Item> <Item Name="PubTypeList" Type="List"> <Item Name="PubType" Type="String">Journal Article</Item> </Item> <Item Name="RecordStatus" Type="String">PubMed - indexed for MEDLINE</Item> <Item Name="PubStatus" Type="String">ppublish</Item> <Item Name="ArticleIds" Type="List"> <Item Name="pubmed" Type="String">9039911</Item> <Item Name="doi" Type="String">10.1038/385810a0</Item> <Item Name="eid" Type="String">9039911</Item> <Item Name="rid" Type="String">9039911</Item> </Item> <Item Name="DOI" Type="String">10.1038/385810a0</Item> <Item Name="History" Type="List"> <Item Name="pubmed" Type="Date">1997/02/27 00:00</Item> <Item Name="medline" Type="Date">1997/02/27 00:01</Item> <Item Name="entrez" Type="Date">1997/02/27 00:00</Item> </Item> <Item Name="References" Type="List"> <Item Name="Comment in" Type="String">Nature. 1997 Mar 13;386(6621):119. PMID: 9062180</Item> <Item Name="Comment in" Type="String">Nature. 1997 Apr 3;386(6624):431. PMID: 9087390</Item> <Item Name="Comment in" Type="String">Nature. 2006 Apr 27;440(7088):1112. PMID: 16641972</Item> <Item Name="Comment in" Type="String">Nature. 1997 Jun 19;387(6635):754. PMID: 9194550</Item> <Item Name="Comment in" Type="String">Nature. 1997 Feb 27;385(6619):753. PMID: 9039891</Item> <Item Name="Comment in" Type="String">Nature. 1997 Mar 6;386(6620):12. PMID: 9052771</Item> <Item Name="Comment in" Type="String">Nature. 1997 Apr 3;386(6624):431. PMID: 9087392</Item> <Item Name="Erratum in" Type="String">Nature 1997 Mar 13;386(6621):200</Item> </Item> <Item Name="HasAbstract" Type="Integer">1</Item> <Item Name="PmcRefCount" Type="Integer">460</Item> <Item Name="FullJournalName" Type="String">Nature</Item> <Item Name="ELocationID" Type="String"></Item> <Item Name="SO" Type="String">1997 Feb 27;385(6619):810-3</Item> </DocSum> </eSummaryResult>
When you want to create a link, use [[pubmed>9039911]]. → 9039911
Recent version of DokuWiki has Extention manager that can download and install plugin automatically. Use the manager.
This DokuWiki plugin formats a molecular formula by using 'chem' tag.
| Appearance | DokuWiki code | memo |
|---|---|---|
| C2H6 | <chem>C2H6</chem> | |
| Na2HPO4 12H2O | <chem>Na2HPO4 12H2O</chem> | |
| Al2(SO4)3 | <chem>Al2(SO4)3</chem> | Using brackets |
| C2H5O2-Na+ | <chem>C2H5O2|-Na+</chem> | Inserted a pipe before a formal charge. |
| Cl2H6N2Pt2+ | <chem>Cl2H6N2Pt2+</chem> | Formal charge number before +/-. |
| [(C6H4)2]412+ | <chem>[(C6H4)2]4|12+</chem> | Using several combinations |
Usage of seperation between atom-numbers and charge-numbers
| Appearance | code | memo |
|---|---|---|
| SO42- | <chem>SO4|2-</chem> | Correctly formated |
| SO42- | <chem>SO42-</chem> | Needs a pipe between 4 and 2. |
| SO4 2- | <chem>SO4 2-</chem> | Undesired white space |
You can install by using 'Manager Plugins' in Admin tools. Download URL is available at https://www.dokuwiki.org/plugin:chem.
(Kibi posted bug-fix and made some extension for isotope expression in the previous system of DW. Since a 'discussion plugin' is not deployed in this current DW, I pasted his/her comment here. Thanks, Kibi — i.obataya 2009/11/11 19:17)
I've made some improvements to your plugin: now it can handle not only charge number of ion, but oxidation state: N-3, N-1, N0, N+1, N+3, H2+1S+6O3-2S-2
Fixed error with “+” in equation: 2H2 + O2 ⇒ 2H2O
Fixed error with alternative formulas like Anion2Cation3
Added support of isotope numbers: 238U, 2239Pu
All you need is replace function getChemFormat with that:
function getChemFormat($raw){ $pattern = array("/([A-Za-z\]\)]+)(0)/", "/[\|]?([0-9]*)[\^]/", "/([^ ][\]\)]?)[\|]?(([\-\+][0-9]*)|([0-9]*[\-\+]))/", "/([A-Z]|[a-z]|\)|\])([1-9][0-9]*)/"); $replace = array("\${1}<sup>\${2}</sup>", "<sup>\${1}</sup>", "\${1}<sup>\${2}</sup>","\${1}<sub>\${2}</sub>"); return preg_replace($pattern,$replace,$raw); }
The examples ahead would be like this: