Advanced Editing of Pathway/Genome Databases. Ron Caspi. General Curation. User Preferences. Create and Use Author and Organization Frames. Using the Text Editor. Formatting <i> italic </i>, <b> bold </i> know your α, β Text wrapper: need two newlines to force a new paragraph
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example: Putrescin Biosynthesis
Specified in the Pathway Info Editor
Enzymes Not Used : useful when an enzyme is associated with a reaction, but does not participate in a specific pathway. For example, a catabolic enzyme in a biosynthetic pathway (e.g. EC 220.127.116.11, ornithine carbamoyltransferase)
Hypothetical reactions: useful when a pathway step is proposed, but has not been proven
is composed of:
The frame editor is powerful, but dangerous… Use it when there are no alternatives.
Adenosylmethionine decarboxylase is first synthesized as a proenzyme, and then self-cleaves into two smaller polypeptides. Each cleavage product forms a homotetramer, and the two complexes form a heterooctamer.
A combination of editors enables creation of such multi-level complexes.
Tutorial: Creating Protein Complexes
Modifications of MetaCyc classes is considered a schema change, and will be overwritten during the next update!
Only use this procedure to correct curation errors that were introduced in your PGDB!
Tutorial: the Ontology Editor
Consistency Checking should be performed routinely (every few months), and detected problems should be addressed
MetaCyc pathways are extensively linked to other pathways. When new PGDBs are created by Pathologic, these links are still there, even if they point to pathways that are not present in the new PGDB. These links are only removed by the Consistency Checker.
Example: create an empty |FRAME: | construct, then run the task “Check Frame References”
(optional inclusion of enzymes and genes)
The following commands will import a frame from MetaCyc to EcoCyc:
Both databases must be open before this will work.
example: folate polyglutamylation I
The process of uploading a PGDB to the Registry is largely automated. See “Publishing PGDBs in the Registry” in the User Guide for details