XML essentials (PDF) - Chagall

This document presents a quick introduction to XML, as used for the submission
of structured information into the SigPath information management system (IMS).
Please see the SigPath CD-ROM for electronic versions of the files discussed
here. The CD-ROM also features animated tutorials that explain how to submit
XML files to SigPath, and other useful ways to interact with the SigPath IMS to
manage interactions and quantitative data in support the biochemical modeling
efforts.
XML essentials
XML stands for EXtensible Markup Language. XML is a language used to
represent data and structured information. The information management
approach implemented in SigPath uses XML extensively to support advanced
information submissions.
An XML documents contains XML markup elements, elements for short, or tags.
An element looks like this: , or , or again, .
An element is an identifier enclosed in brackets (‘’).
A valid XML document contains one root element, as shown in the following
document:
Document 1.
Note the structure of comments in the previous example, and how elements are
indented to illustrate the parent-child relation among elements. The same
structure is shown below in a graphical format:
root
element
boat
Fabien Campagne, October 8 th 2003. For up-to-date information, please visit:
http://www.sigpath.org/
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XML elements can have attributes (e.g., attribute=”” or size=””). Attributes are
often used to describe properties of the element, such as size and color of the
“boat” element in Document 1.
Together with the ability to create a hierarchy of elements, these features make it
possible to represent a variety of information.
For instance, Document 2, below, illustrates how data and information can be
represented in XML and shows that text can be used as a child of element (see
).

Many software tools support XML schemas. An XML schema defines what
constitutes a valid XML document. For instance, a schema is used to define the
name of the root element for documents that contain submissions for SigPath.
According to the current SigPath schema, the root element of valid XML
information exchange documents must be named .
The SigPath submission schema describes many more constraints on
submission documents. These constraints are useful to remove ambiguity and
assist users in building consistent submissions.
A complete description of the SigPath schema is accessible from the Project web
site: Open http://www.sigpath.org/ and click on the “SigPath XML schema” link on
the menu bar (top left of the page).
Figure 1. The SigPath XML Schema page is shown. The page presents the
schema documentation, a link to the most recent schema and XML submission
examples.
Fabien Campagne, October 8 th 2003. For up-to-date information, please visit:
http://www.sigpath.org/
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Click on “XML schema documentation” to access details about what constitutes a
valid SigPath submission document. You should see something like shown on
Figure 2.
Click on this link to see
the root element for
SigPath documents.
Figure 2. Overview of the documentation for the element.
Fabien Campagne, October 8 th 2003. For up-to-date information, please visit:
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Figure 3. Root element of SigPath submission documents. Elements on the right
are children of the root element, and must occur in sequence, with the given
multiplicity (e.g., 0...∞ for elements that can occur zero or more times).
Beyond documentation shown on Figure 2 and 3, XML Schemas are formally
defined in XML Schema files. Such files (generally named with an .xsd
extension) can be used in XML editors to dynamically check that a document is
valid, or to provide contextual help or support for element completion while
creating a document manually.
Fabien Campagne, October 8 th 2003. For up-to-date information, please visit:
http://www.sigpath.org/
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The SigPath XML Schema can be downloaded from the second link shown on
Figure 1. The next section will show how to use this schema to create a reaction
submission file.
Zooming on the molecule element
The schema documentation is shown on Figure 4 for the molecule element. This
element makes it possible to uniquely identify molecules in the current
submission file or in SigPath, to include them in reactions, models, or other
entities represented in SigPath.
According to the documentation, the following three constructs are valid. Each of
them can be used to match a molecule in the database or in the current
submission file.
(a)
(b)
(c)
(a) Can be used to match a molecule which was previously submitted to
SigPath, for instance a complex, that does not exist in another database.
(b) Can be used to match proteins or small molecules that exist in other
databases and have been imported in SigPath (these proteins are part of
what we call background information).
(c) Can be used to reference a molecule that is defined in the current XML
submission file. The attribute ‘idref’ must match the attribute ‘id’ of one
(and only one) molecule definition element in the SigPath submission file.
A combination of (a), (b) and (c) is allowed by the schema. In this case, priority
rules apply: idref is considered first. When idref does not match any molecule,
accession code and organisms are used. If no match is found, spid is finally
considered. When no match can be found, an error is reported.
In the context of an enzymatic reaction, the following attributes can also be used:
(d)
(e)
(d) The attribute isSubstrate=”true” indicates that the molecule acts as a
substrate of the enclosing enzymatic reaction.
(e) Similarly, isProduct=”true” indicates that the molecule acts as a product of
the enclosing enzymatic reaction.
Fabien Campagne, October 8 th 2003. For up-to-date information, please visit:
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Figure 4. SigPath schema documentation for the element. Diagram
shows that the molecule element is a sequence of interaction_site, name and
description elements. When browsing the documentation online, clicking on an
element displays a detailed view such as the one shown for molecule. The “used
by” row shows in which context a molecule element can appear in a SigPath
submission. The “attributes” row presents the elements of the molecule element.
Importing XML submission into SigPath
To submit this reaction into SigPath, follow these steps:
1. Navigate to the production instance of SigPath (start from
http://www.sigpath.org/, use the menu on the left to access production).
2. Click on the link “Submit Data via XML Upload”.
3. Login (registering is free and helps identify submitters and reviewers).
4. You should see a page that contains what is shown on Figure 5.
Figure 5. Submitting information in the SigPath XML format.
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5. Click “Browse” to locate the file that contains the XML submission (you
can create this file by copying the content of Document 3 to an empty xml
file, for instance).
6. Press “Submit” when you have located the XML submission file.
7. The XML submission will be checked for errors and inconsistencies.
Errors will be reported. The page shown in Figure 6 will be displayed. Any
error will be shown highlighted in yellow in the submission file.
8. Correct any error and resubmit (to avoid schema validation errors it is best
to use a validating XML schema editor, to check the submission against
the schema).
9. When no errors are detected, the display will change to Figure 6. Press
Confirm Data Submission to save the submission into SigPath.
Figure 6. Confirmation step for XML submission.
Fabien Campagne, October 8 th 2003. For up-to-date information, please visit:
http://www.sigpath.org/
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Submitting a binding reaction
The document needed to submit a binding reaction into SigPath is shown on
Document 3. Follow the steps shown in the previous section to submit this
reaction. The elements shown in Document 3 will be reviewed during the tutorial.
Figure 7 shows the hierarchy of elements in this submission.
Grb2-Sos
This is the reaction that creates the complex.
Document 3. Grb2 + Sos ↔ Grb2.Sos
sigpath-submission
components
reaction
complex (define)
left
right
molecule
molecule
complex (reference)
Figure 7. Structure of Document 3. Note how a complex is explicitly defined (on
the left, underneath components) before it is used on the right side of the
reaction. Complexes cannot be defined by themselves. They must appear in at
least one reaction of the form A + B ↔ Complex(A,B).
Fabien Campagne, October 8 th 2003. For up-to-date information, please visit:
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Submitting an enzymatic reaction
The document needed to submit an enzymatic reaction into SigPath is shown in
Document 4. Follow the steps shown in “Importing XML submission into
SigPath” to submit this reaction. The elements shown in Document 4 will be
reviewed during the tutorial.
P-CREB_RAT
protein
CREB_RAT
milliM-1.sec-1
1.0
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micromoles/l
20.0
sec-1
0.1
Document 4. CREB-RAT + ATP → P-CREB_RAT + ADP [enzyme : MAPK2]
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http://www.sigpath.org/
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