Portal:IEM

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Inborn Errors of Metabolism Portal

This portal is set up to give an overview of all Inborn Errors of Metabolism (IEM) pathways. This portal is also featured in the latest NAR Database Issue on WikiPathways.

IMPORTANT: the current list of pathways is based on the currently published (2014) 4th edition of the book (ISBN 3642403360 (978-3642403361)). There is a new edition(5) upcoming and the pathways in the new edition are being digitized in a collaboration with the chapter authors, but these have no been made public yet, and therefore do not show up here.

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Covered Pathways

Chapter ed. 5 Title Links WP Chapter ed. 4 Status Diseases: x from ch. ed. 4
(+y) from other ch.
13 Disorders of pyrimidine and purine metabolism WP4225 and WP4224 41 Approved
16 Disorders of glutathione metabolism WP4518 42 Approved
17 Disorders of ammonia detoxification WP4595 4 Approved
18 Disorders of amino acid transport WP5029 6 In Progress
19 Disorders of monoamine metabolism WP4220 31 Approved
20 Disorders of phenylalanine and tetrahydrobiopterin metabolism WP4156 1 Approved 7 (+3), non missing
21 Disorders of tyrosine metabolism WP4506 2 Approved 5, non missing
22 Disorders of sulfur amino acid and sulfide metabolism WP4292 3 Approved 7, non missing
23 Disorders of branched-chain amino acid metabolism WP4686 7 In Progress
26 Disorders of glycine metabolism Fig.5.1:WP5028,
Fig.5.2: WP4688,
Fig.5.3:WP4157,
Fig.5.4: WP5026
5 In Progress
28 Disorders of cobalamin metabolism WP4271 13 Approved
29 Disorders of folate metabolism WP4259 and WP4288 10 Approved
30 Disorders of biotin metabolism WP5031 14 Approved
31 Disorders of thiamine metabolism WP4297 15 Approved
32 Disorders of riboflavin metabolism WP5037 16 Approved
34 Vitamin B6 -Dependent and Responsive Disorders WP4228 11 Approved
35 Disorders of molybdenum metabolism WP4507 and WP4504 12 Approved
42 Disorders of pyruvate and Krebs cycle metabolism WP4236 20 Approved
47 Primary CoQ10 deficiencies WP5037 16 Approved
53 Disorders of lipoprotein metabolism WP4522 43 Approved
55 Disorders of steroid metabolism WP4523 and WP4524 37 Approved
60 Lysosomal storage disorders WP4153 25 Approved
66 Congenital disorders of N-linked and O-linked glycosylation WP4521 30 Approved
69 Cerebral organic acidurias WP4519 and WP5030 8 & 9 Approved
 ? Disorders of phosphoinositide metabolism WP4971  ? Approved
 ? Oxysterols derived from cholesterol WP4545  ? Approved


Information on Pathway Curation:

This Table provides an overview of which chapters have been covered by WikiPathways. Approved pathways are coloured blue; pathways which still need work (however are a part of the database) are coloured orange.


Tip:

Click on the arrows behind the Table headers to sort this table based on Chapter number (edition 4 and 5 available), title, WikiPathways reference and Curation Status.


Pathway Visualisations

View all digitized Pathways from the Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases by Blau et al. (see it on Scholia.)


How to add a pathway to the portal

The list of Featured Pathways is not static and can be updated at any time. If you know of a pathway that should be added, please contact Denise Slenter.


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Data Analysis

With the pathways from the Blau book (as well as with other pathways on WikiPathways), various data analysis approaches can be performed.

For the current overview of which pathways are covered and their status, see here.

To download all pathways tagged for Inborn Errors of Metabolsim as GPML, click here.

For example scripts (in R), please visit PathwayAnalysisBlauBook.

The Figure on the left shows an example of network analysis with Cytoscape, where known drug-target interactions from DrugBank using the CyTargetLinker app have been added to the purine metabolism pathway.

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Featured Pathway

Disorders of the Krebs cycle (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/f/fe/WP4236_112007.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/f/fe/WP4236_112007.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Disorders of th...', 'https://www.wik...', 'Disorders of th...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4236', '300', 'center', 'Disorders of th...', 'pathway', 'Disorders of th...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Sunday 11 April...', 'Portal:IEM/Feat...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/Article.php(3406): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 112007)
  32. 31 /var/www/wikipathways/includes/Article.php(875): Article->outputWikiText('{{{{FULLPAGENAM...', false)
  33. 32 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  34. 33 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  35. 34 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  36. 35 {main}
View all Featured Pathways for this Portal

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News

  • Winter 2020: All images of the first 15 chapters are available on WikiPathways.
  • Summer 2020: An overview of all covered chapter has been created on the main page
  • Spring 2020: The Portal has been created
  • Autumn 2019: Several chapters of the new book have already been digitized (but are embargoed)


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