Difference between revisions of "iRefIndex Development"
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| + | {{Note| | ||
| + | This page describes development processes related to the code supporting iRefIndex release 9 and earlier. | ||
| + | }} | ||
| + | |||
See [[iRefIndex Issues and Notes]] for details of ongoing work to improve the iRefIndex software. | See [[iRefIndex Issues and Notes]] for details of ongoing work to improve the iRefIndex software. | ||
| Line 5: | Line 9: | ||
# Identify the location of the downloaded data. | # Identify the location of the downloaded data. | ||
# Evaluate the form of the data: | # Evaluate the form of the data: | ||
| − | # | + | #* For PSI MI XML (Molecular Interaction XML) documents, check the version of the format employed by the data documents. |
| − | # | + | #* For the specific version, review the format's schema and how the data uses the schema. For example, PSI MI XML permits the specification of interactors within interaction descriptions as well as in a separate interactor list. |
| + | #* For MITAB files, see [[iRefIndex MITAB Mapping]]. | ||
# Review existing, similar mapper definition files. | # Review existing, similar mapper definition files. | ||
=== Evaluating the Data === | === Evaluating the Data === | ||
| − | The <tt>show_xml_paths.py</tt> script in the <tt>iRef_PSI_XML2RDBMS</tt> directory can be used to show the different element paths used in an XML data file to hold data items. For example: | + | The <tt>show_xml_paths.py</tt> script in the <tt>tools</tt> directory within the <tt>iRef_PSI_XML2RDBMS</tt> directory can be used to show the different element paths used in an XML data file to hold data items. For example: |
| − | python show_xml_paths.py --data /home/irefindex/data/MINT/2010-09-14/10023771.psi25.xml | + | python tools/show_xml_paths.py --data /home/irefindex/data/MINT/2010-09-14/10023771.psi25.xml |
The resulting list of paths indicates the places in the element hierarchy of a PSI-MI XML file where information is actually stored. For example: | The resulting list of paths indicates the places in the element hierarchy of a PSI-MI XML file where information is actually stored. For example: | ||
| Line 298: | Line 303: | ||
The mapper files already in existence can be reviewed by using the <tt>show_xml_paths.py</tt> script together with one of these files which reside in the <tt>mapper</tt> subdirectory of the <tt>iRef_PSI_XML2RDBMS</tt> directory. For example: | The mapper files already in existence can be reviewed by using the <tt>show_xml_paths.py</tt> script together with one of these files which reside in the <tt>mapper</tt> subdirectory of the <tt>iRef_PSI_XML2RDBMS</tt> directory. For example: | ||
| − | python show_xml_paths.py --mapper mapper/Map25_CORUM.xml | + | python tools/show_xml_paths.py --mapper mapper/Map25_CORUM.xml |
The resulting output describes the structure of the data and how the mapper will attempt to interpret that data. For example (for CORUM): | The resulting output describes the structure of the data and how the mapper will attempt to interpret that data. For example (for CORUM): | ||
| Line 551: | Line 556: | ||
The definitions involved can then be incorporated into the new mapper file, adjusting identifiers appropriately. Although the <tt>hostOrganism</tt> data in the above example originates from a different place in the element hierarchy, a simple path alteration to point to a location in the <tt>interactionList</tt> hierarchy is probably sufficient to make the initial mapping definitions consistent with the newly incorporated definitions for <tt>interactionDetectionMethod</tt> - the <tt>grouper</tt> identifiers for the mapping definitions refer to <tt>experimentDescription</tt> in all cases. | The definitions involved can then be incorporated into the new mapper file, adjusting identifiers appropriately. Although the <tt>hostOrganism</tt> data in the above example originates from a different place in the element hierarchy, a simple path alteration to point to a location in the <tt>interactionList</tt> hierarchy is probably sufficient to make the initial mapping definitions consistent with the newly incorporated definitions for <tt>interactionDetectionMethod</tt> - the <tt>grouper</tt> identifiers for the mapping definitions refer to <tt>experimentDescription</tt> in all cases. | ||
| + | |||
| + | === Defining the Database Identifier === | ||
| + | |||
| + | A new database identifier is required for new data sources. Source identifiers are defined in each data source's configuration file in the <tt>source</tt> element. For example, for InnateDB: | ||
| + | |||
| + | <pre> | ||
| + | <specs> | ||
| + | <source>InnateDB</source> | ||
| + | <filetype>.xml</filetype> | ||
| + | </specs> | ||
| + | </pre> | ||
| + | |||
| + | These identifiers are then mapped to database identifiers in the iRefIndex <tt>int_db</tt> table. Thus, an <tt>int_db</tt> record must be defined, assigning a database identifier (an integer) which corresponds to this source identifier. | ||
| + | |||
| + | To define a new database identifier the <tt>Create_iRefIndex.sql</tt> file, which resides in the <tt>SQL</tt> directory of the <tt>BioPSI_Suplimenter</tt> software distribution, must be modified, adding a new statement as follows: | ||
| + | |||
| + | INSERT INTO int_db(id,name) VALUES(<database identifier>,'<source identifier>'); | ||
| + | |||
| + | For example: | ||
| + | |||
| + | INSERT INTO int_db(id,name) VALUES(178,'InnateDB'); | ||
| + | |||
| + | === Re-running the Parser === | ||
| + | |||
| + | If data files have already been parsed, but the development process dictates that they be parsed again, potentially to populate a test database, it is necessary to delete various files which are written to the filesystem by the parser in order to prevent repeated parsing of data. These files are called <tt>lastUpdate.obj</tt> and contain information about previous parsing operations. | ||
| + | |||
| + | find /home/irefindex/data -name lastUpdate.obj | xargs rm | ||
| + | |||
| + | === Modifying Generated Data === | ||
| + | |||
| + | New sources require changes to some generated data tables and to the programs that populate them: | ||
| + | |||
| + | * In the definition of the <tt>cy_edgeatrib_canonical</tt> table in the <tt>make_canonical_tables.sql</tt> file in the <tt>SQL_commands</tt> directory, a new column is required for each newly defined source. | ||
| + | * The <tt>src/process/no/uio/biotek/Make_Cy_tables.java</tt> file in <tt>BioPSI_Suplimenter</tt> needs to be changed so that the <tt>popCombine_edge</tt> method has a set of statements populating the new column created in the <tt>cy_edgeatrib_canonical</tt> table, and the <tt>src/process/no/uio/biotek/PreProcess_process.java</tt> file also needs changing so that the definition of the <tt>cy_edgeatrib</tt> table in the <tt>commit</tt> method includes a new column for each newly defined source. | ||
| + | * The <tt>make_iRefWeb.sql</tt> file in the <tt>SQL_commands</tt> directory requires a statement defining each new source in the <tt>source_db</tt> table. | ||
== All iRefIndex Pages == | == All iRefIndex Pages == | ||
Latest revision as of 16:04, 26 October 2012
 Note |
This page describes development processes related to the code supporting iRefIndex release 9 and earlier. |
See iRefIndex Issues and Notes for details of ongoing work to improve the iRefIndex software.
Contents
Adding Sources to iRefIndex
- Identify the location of the downloaded data.
- Evaluate the form of the data:
- For PSI MI XML (Molecular Interaction XML) documents, check the version of the format employed by the data documents.
- For the specific version, review the format's schema and how the data uses the schema. For example, PSI MI XML permits the specification of interactors within interaction descriptions as well as in a separate interactor list.
- For MITAB files, see iRefIndex MITAB Mapping.
- Review existing, similar mapper definition files.
Evaluating the Data
The show_xml_paths.py script in the tools directory within the iRef_PSI_XML2RDBMS directory can be used to show the different element paths used in an XML data file to hold data items. For example:
python tools/show_xml_paths.py --data /home/irefindex/data/MINT/2010-09-14/10023771.psi25.xml
The resulting list of paths indicates the places in the element hierarchy of a PSI-MI XML file where information is actually stored. For example:
entrySet/@level entrySet/@minorVersion entrySet/@version entrySet/@xmlns entrySet/@xmlns:xsi entrySet/@xsi:schemaLocation entrySet/entry/experimentList/experimentDescription/@id entrySet/entry/experimentList/experimentDescription/attributeList/attribute entrySet/entry/experimentList/experimentDescription/attributeList/attribute/@name entrySet/entry/experimentList/experimentDescription/attributeList/attribute/@nameAc entrySet/entry/experimentList/experimentDescription/bibref/xref/primaryRef/@db entrySet/entry/experimentList/experimentDescription/bibref/xref/primaryRef/@dbAc entrySet/entry/experimentList/experimentDescription/bibref/xref/primaryRef/@id entrySet/entry/experimentList/experimentDescription/bibref/xref/primaryRef/@refType entrySet/entry/experimentList/experimentDescription/bibref/xref/primaryRef/@refTypeAc entrySet/entry/experimentList/experimentDescription/hostOrganismList/hostOrganism/@ncbiTaxId entrySet/entry/experimentList/experimentDescription/hostOrganismList/hostOrganism/names/fullName entrySet/entry/experimentList/experimentDescription/hostOrganismList/hostOrganism/names/shortLabel entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/names/alias entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/names/alias/@type entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/names/alias/@typeAc entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/names/fullName entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/names/shortLabel entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/xref/primaryRef/@db entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/xref/primaryRef/@dbAc entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/xref/primaryRef/@id entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/xref/primaryRef/@refType entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/xref/primaryRef/@refTypeAc entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/xref/secondaryRef/@db entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/xref/secondaryRef/@dbAc entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/xref/secondaryRef/@id entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/xref/secondaryRef/@refType entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/xref/secondaryRef/@refTypeAc entrySet/entry/experimentList/experimentDescription/names/fullName entrySet/entry/experimentList/experimentDescription/names/shortLabel entrySet/entry/experimentList/experimentDescription/xref/primaryRef/@db entrySet/entry/experimentList/experimentDescription/xref/primaryRef/@dbAc entrySet/entry/experimentList/experimentDescription/xref/primaryRef/@id entrySet/entry/experimentList/experimentDescription/xref/primaryRef/@refType entrySet/entry/experimentList/experimentDescription/xref/primaryRef/@refTypeAc entrySet/entry/experimentList/experimentDescription/xref/secondaryRef/@db entrySet/entry/experimentList/experimentDescription/xref/secondaryRef/@dbAc entrySet/entry/experimentList/experimentDescription/xref/secondaryRef/@id entrySet/entry/experimentList/experimentDescription/xref/secondaryRef/@refType entrySet/entry/experimentList/experimentDescription/xref/secondaryRef/@refTypeAc entrySet/entry/interactionList/interaction/@id entrySet/entry/interactionList/interaction/attributeList/attribute entrySet/entry/interactionList/interaction/attributeList/attribute/@name entrySet/entry/interactionList/interaction/attributeList/attribute/@nameAc entrySet/entry/interactionList/interaction/confidenceList/confidence/unit/names/fullName entrySet/entry/interactionList/interaction/confidenceList/confidence/unit/names/shortLabel entrySet/entry/interactionList/interaction/confidenceList/confidence/unit/xref/primaryRef/@db entrySet/entry/interactionList/interaction/confidenceList/confidence/unit/xref/primaryRef/@dbAc entrySet/entry/interactionList/interaction/confidenceList/confidence/unit/xref/primaryRef/@id entrySet/entry/interactionList/interaction/confidenceList/confidence/unit/xref/primaryRef/@refType entrySet/entry/interactionList/interaction/confidenceList/confidence/unit/xref/primaryRef/@refTypeAc entrySet/entry/interactionList/interaction/confidenceList/confidence/value entrySet/entry/interactionList/interaction/experimentList/experimentRef entrySet/entry/interactionList/interaction/interactionType/names/fullName entrySet/entry/interactionList/interaction/interactionType/names/shortLabel 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entrySet/entry/interactionList/interaction/participantList/participant/participantIdentificationMethodList/participantIdentificationMethod/xref/secondaryRef/@refType entrySet/entry/interactionList/interaction/participantList/participant/participantIdentificationMethodList/participantIdentificationMethod/xref/secondaryRef/@refTypeAc entrySet/entry/interactionList/interaction/participantList/participant/xref/primaryRef/@db entrySet/entry/interactionList/interaction/participantList/participant/xref/primaryRef/@dbAc entrySet/entry/interactionList/interaction/participantList/participant/xref/primaryRef/@id entrySet/entry/interactionList/interaction/participantList/participant/xref/primaryRef/@refType entrySet/entry/interactionList/interaction/participantList/participant/xref/primaryRef/@refTypeAc entrySet/entry/interactionList/interaction/xref/primaryRef/@db entrySet/entry/interactionList/interaction/xref/primaryRef/@dbAc entrySet/entry/interactionList/interaction/xref/primaryRef/@id entrySet/entry/interactionList/interaction/xref/primaryRef/@refType entrySet/entry/interactionList/interaction/xref/primaryRef/@refTypeAc entrySet/entry/interactorList/interactor/@id entrySet/entry/interactorList/interactor/attributeList/attribute entrySet/entry/interactorList/interactor/attributeList/attribute/@name entrySet/entry/interactorList/interactor/attributeList/attribute/@nameAc entrySet/entry/interactorList/interactor/interactorType/names/fullName entrySet/entry/interactorList/interactor/interactorType/names/shortLabel entrySet/entry/interactorList/interactor/interactorType/xref/primaryRef/@db entrySet/entry/interactorList/interactor/interactorType/xref/primaryRef/@dbAc entrySet/entry/interactorList/interactor/interactorType/xref/primaryRef/@id entrySet/entry/interactorList/interactor/interactorType/xref/primaryRef/@refType entrySet/entry/interactorList/interactor/interactorType/xref/primaryRef/@refTypeAc entrySet/entry/interactorList/interactor/interactorType/xref/secondaryRef/@db entrySet/entry/interactorList/interactor/interactorType/xref/secondaryRef/@dbAc entrySet/entry/interactorList/interactor/interactorType/xref/secondaryRef/@id entrySet/entry/interactorList/interactor/interactorType/xref/secondaryRef/@refType entrySet/entry/interactorList/interactor/interactorType/xref/secondaryRef/@refTypeAc entrySet/entry/interactorList/interactor/names/alias entrySet/entry/interactorList/interactor/names/alias/@type entrySet/entry/interactorList/interactor/names/alias/@typeAc entrySet/entry/interactorList/interactor/names/fullName entrySet/entry/interactorList/interactor/names/shortLabel entrySet/entry/interactorList/interactor/organism/@ncbiTaxId entrySet/entry/interactorList/interactor/organism/names/fullName entrySet/entry/interactorList/interactor/organism/names/shortLabel entrySet/entry/interactorList/interactor/sequence entrySet/entry/interactorList/interactor/xref/primaryRef/@db entrySet/entry/interactorList/interactor/xref/primaryRef/@dbAc entrySet/entry/interactorList/interactor/xref/primaryRef/@id entrySet/entry/interactorList/interactor/xref/primaryRef/@refType entrySet/entry/interactorList/interactor/xref/primaryRef/@refTypeAc entrySet/entry/interactorList/interactor/xref/primaryRef/@version entrySet/entry/interactorList/interactor/xref/secondaryRef/@db entrySet/entry/interactorList/interactor/xref/secondaryRef/@dbAc entrySet/entry/interactorList/interactor/xref/secondaryRef/@id entrySet/entry/interactorList/interactor/xref/secondaryRef/@refType entrySet/entry/interactorList/interactor/xref/secondaryRef/@refTypeAc entrySet/entry/interactorList/interactor/xref/secondaryRef/@secondary entrySet/entry/interactorList/interactor/xref/secondaryRef/@version entrySet/entry/source/@releaseDate entrySet/entry/source/attributeList/attribute entrySet/entry/source/attributeList/attribute/@name entrySet/entry/source/attributeList/attribute/@nameAc entrySet/entry/source/names/fullName entrySet/entry/source/names/shortLabel entrySet/entry/source/xref/primaryRef/@db entrySet/entry/source/xref/primaryRef/@dbAc entrySet/entry/source/xref/primaryRef/@id entrySet/entry/source/xref/primaryRef/@refType entrySet/entry/source/xref/primaryRef/@refTypeAc entrySet/entry/source/xref/primaryRef/@secondary entrySet/entry/source/xref/secondaryRef/@db entrySet/entry/source/xref/secondaryRef/@dbAc entrySet/entry/source/xref/secondaryRef/@id entrySet/entry/source/xref/secondaryRef/@refType entrySet/entry/source/xref/secondaryRef/@refTypeAc
With this information, a suitable mapper file can be identified for the conversion of the XML-encoded data into tabular data to be stored in a database. In the above example, it is apparent that the experiment, interaction and interactor details reside alongside each other within each entry element:
entrySet/entry/experimentList/experimentDescription entrySet/entry/interactionList/interaction entrySet/entry/interactionList/interaction/participantList/participant entrySet/entry/interactorList/interactor
In contrast, other PSI-MI XML files adopt a different structure which can be reduced to the following:
entrySet/entry/interactionList/interaction entrySet/entry/interactionList/interaction/experimentList/experimentDescription entrySet/entry/interactionList/interaction/participantList/participant
The different sources can be divided into a number of subformats as follows:
| Subformat | Sources | Notes |
|---|---|---|
| Separate experiment, interaction, interactor lists | BioGRID, HPRD, IntAct, MINT, OPHID | BioGRID uses proteininteractor instead of interactor OPHID uses proteinParticipant, proteinInteractor |
| Interaction contains experiment; separate interactor list | DIP | |
| Interaction contains experiment and interactor/participant | BIND Translation, CORUM, InnateDB, MatrixDB, MPACT, MPPI | InnateDB provides apparently redundant lists of experiments and interactors MPPI uses proteinParticipant, proteinInteractor |
Reviewing Mapper Files
The mapper files already in existence can be reviewed by using the show_xml_paths.py script together with one of these files which reside in the mapper subdirectory of the iRef_PSI_XML2RDBMS directory. For example:
python tools/show_xml_paths.py --mapper mapper/Map25_CORUM.xml
The resulting output describes the structure of the data and how the mapper will attempt to interpret that data. For example (for CORUM):
Element experimentDescription ...
Table int_name ...
_euid ...
<incremental>
_idetlbl ...
entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/names/shortLabel
entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/names/alias
entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/names/fullname
_idetncat ...
24
25
25
Table int_xref ...
_euid ...
<incremental>
_brefdb ...
entry/interactionList/interaction/experimentList/experimentDescription/bibref/xref/primaryRef/@db
entry/interactionList/interaction/experimentList/experimentDescription/bibref/xref/secondaryRef/@db
_brefid ...
entry/interactionList/interaction/experimentList/experimentDescription/bibref/xref/primaryRef/@id
entry/interactionList/interaction/experimentList/experimentDescription/bibref/xref/secondaryRef/@id
_brefct ...
4
5
Table int_xref ...
_euid ...
<incremental>
_idetdb ...
entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/xref/primaryRef/@db
entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/xref/secondaryRef/@db
_idetid ...
entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/xref/primaryRef/@id
entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/xref/secondaryRef/@id
_idetct ...
6
7
Element experimentList ...
Table int_experiment ...
_euidr ...
_euid
_iuider ...
_iuid
Element interaction ...
Table int_name ...
_iuid ...
<incremental>
_iuiflnm ...
entry/interactionList/interaction/names/fullName
_iuiflnmct ...
12
Table int_source ...
_iuid ...
<incremental>
_itp ...
entry/interactionList/interaction/xref
_isrc ...
entry/interactionList/interaction/xref
_ifle ...
entry/interactionList/interaction/xref
Table int_xref ...
_iuid ...
<incremental>
_idb ...
entry/interactionList/interaction/xref/primaryRef/@db
_iref ...
entry/interactionList/interaction/xref/primaryRef/@id
_irefcat ...
0
Element participant ...
Table int_name ...
_ouid ...
<incremental>
_olb ...
entry/interactionList/interaction/participantList/participant/interactor/names/shortLabel
entry/interactionList/interaction/participantList/participant/interactor/names/alias
entry/interactionList/interaction/participantList/participant/interactor/names/fullName
_olbct ...
13
14
15
Table int_object ...
_ouid ...
<incremental>
_oltyp ...
entry/interactionList/interaction/participantList/participant/interactor/interactorType/names/shortLabel
_osrc ...
entry/interactionList/interaction/participantList/participant/interactor/names
_ofil ...
entry/interactionList/interaction/participantList/participant/interactor/names
Table int_sequence ...
_ouid ...
<incremental>
_obsq ...
entry/interactionList/interaction/participantList/participant/interactor/sequence
Table int_xref ...
_ouid ...
<incremental>
_odb ...
entry/interactionList/interaction/participantList/participant/interactor/xref/primaryRef/@db
entry/interactionList/interaction/participantList/participant/interactor/xref/secondaryRef/@db
_orefid ...
entry/interactionList/interaction/participantList/participant/interactor/xref/primaryRef/@id
entry/interactionList/interaction/participantList/participant/interactor/xref/secondaryRef/@id
_oicat ...
2
3
_otax ...
entry/interactionList/interaction/participantList/participant/interactor/organism/@ncbiTaxId
_otp ...
entry/interactionList/interaction/participantList/participant/interactor/xref/primaryRef/@refType
entry/interactionList/interaction/participantList/participant/interactor/xref/secondaryRef/@refType
Element participantList ...
Table int_source2object ...
_iuidr ...
_iuid
_what ...
entry/interactionList/interaction/participantList/participant/interactor/names
_isrcr ...
entry/interactionList/interaction/participantList/participant/interactor/names
_ifler ...
entry/interactionList/interaction/participantList/participant/interactor/names
_refob ...
_ouid
Adapting an Existing Mapper File
Given an analysis of the data and the identification of the data's "subformat" (explained above), it should be possible to take an existing mapper file which supports the same subformat and to modify it to understand the new data source. For example, the InnateDB data resembles the data of various other sources (listed in the table above), and some comparisons of the structure of the data can be performed to see which source is closest in structure to InnateDB by using a diff-like program, potentially a graphical program such as kompare or kdiff3.
Once a similar source has been identified, the corresponding mapper file can be copied and modified. For example:
cp mapper/Map25_CORUM.xml mapper/Map25_InnateDB.xml
Then, it is necessary to update the new mapper file with details that differ from those in the closest source. In some cases, it can also be useful to consult other mapper files. For example, the following path may not be present in the CORUM mapper file despite being provided by the data file:
entry/experimentList/experimentDescription/hostOrganismList/hostOrganism
However, such information can be used by iRefIndex and may be supported by other mapper files. We may therefore decide to incorporate such information into our new mapper file (and perhaps into CORUM's mapper file, too). To do so, we first inspect other mapper files for the presence of such information and then isolate the section which supports its retrieval. For example, from the IntAct mapper file, using the show_xml_paths.py script...
python show_xml_paths.py --mapper mapper/Map25_INTACT_MINT_BIOGRID.xml --verbose
Here, the --verbose flag provides identifier information which makes finding the element, table and mapping definitions easier:
Element experimentDescription (grouper/id=3)...
[...]
Table int_name (sqlref/id=23)...
_euid ...
<incremental> (provides experimentDescription)
_exorg ...
entry/experimentList/experimentDescription/hostOrganismList/hostOrganism/@ncbiTaxId
_exorgc ...
38
From the above, it becomes apparent that we need a group definition for elementDescription, and that int_name must be populated according to the stated mappings for _euid, _exorg and _exorgc.
Fortunately, a group definition already exists in our new mapper file:
<group id ="3" element ="experimentDescription" parpos="4" atrib="_AUTO_">
<path></path>
<ref choice="no" />
</group>
Meanwhile, the following table modifying section (corresponding to the identifier 23) must be located in the IntAct mapper file:
<sql id="23" userefs="no" >
<stmt>INSERT INTO int_name(uid,name,category) VALUES ('_euid','_exorg','_exorgc');</stmt>
<variablelist>
<variable name="_euid" ></variable>
<variable name="_exorg"></variable>
<variable name="_exorgc"></variable>
</variablelist>
</sql>
Since no conflicting section (with the same identifier for an sql element) exists in the new mapper file, this can be copied without changes. Then, it is necessary to ensure that mappings for _euid, _exorg and _exorgc are present; the following mappings happen to be found in the IntAct mapper file:
<map id="42" sqlref="23" name="_euid" grouper="3">
<instruct>
<param choice="yes" />
</instruct>
</map>
<map id="43" sqlref="23" name="_exorg" grouper="3">
<instruct>
<readfromfile choice="yes">
<path variable="_exorg" groupTag="ex" usetext="no" attribute="ncbiTaxId">entry,experimentList,experimentDescription,hostOrganismList,hostOrganism</path>
</readfromfile>
</instruct>
</map>
<map id="43" sqlref="23" name="_exorgc" grouper="3">
<instruct>
<readfromfile choice="yes">
<path variable="_exorgc" groupTag="ex" usetext="no" prefix="yes" val="38">entry,experimentList,experimentDescription,hostOrganismList,hostOrganism</path>
</readfromfile>
</instruct>
</map>
Although _euid is a known name in the new mapper file already, no mapper definition exists to connect it to the table modification section (with identifier 23). Thus, it is necessary to copy the above mappings, to adjust their identifiers to avoid conflicts with other mappings, and to make sure that the grouper attributes refer to the correct group definition for experimentDescription. Fortunately, no such adjustments are required in this case and the definitions can be copied directly.
Choosing Sources of Data
In the above example, the hostOrganism information was extracted from the separate experimentList, but in order to maintain consistency with the other sources in the data file, we may choose a different source in the interactionList, particularly since the information appears to be duplicated in that location. Thus, a mapping is required that can extract data from the following path:
entry/interactionList/interaction/experimentList/experimentDescription/hostOrganismList/hostOrganism
Even if a mapping does not exist for the above path, there may be mappings involving similar paths:
entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/names/shortLabel
In this case, a different mapper file should be chosen to provide a suitable definition:
python show_xml_paths.py --mapper mapper/Map25_DIP.xml --verbose
A suitable section of that file can be summarised as follows:
Element experimentDescription (grouper/id=3)...
[...]
Table int_name (sqlref/id=15)...
_euid ...
<incremental> (provides experimentDescription)
_idetlbl ...
(intdetectionshortLabel) ...
entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/names/shortLabel
(intdetectionalias) ...
entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/names/alias
(intdtfull) ...
entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/names/fullName
_idetncat ...
(intdetectionshlacategory) ...
24
(intdetectionoblac) ...
25
(indtcatful) ...
26
The definitions involved can then be incorporated into the new mapper file, adjusting identifiers appropriately. Although the hostOrganism data in the above example originates from a different place in the element hierarchy, a simple path alteration to point to a location in the interactionList hierarchy is probably sufficient to make the initial mapping definitions consistent with the newly incorporated definitions for interactionDetectionMethod - the grouper identifiers for the mapping definitions refer to experimentDescription in all cases.
Defining the Database Identifier
A new database identifier is required for new data sources. Source identifiers are defined in each data source's configuration file in the source element. For example, for InnateDB:
<specs>
<source>InnateDB</source>
<filetype>.xml</filetype>
</specs>
These identifiers are then mapped to database identifiers in the iRefIndex int_db table. Thus, an int_db record must be defined, assigning a database identifier (an integer) which corresponds to this source identifier.
To define a new database identifier the Create_iRefIndex.sql file, which resides in the SQL directory of the BioPSI_Suplimenter software distribution, must be modified, adding a new statement as follows:
INSERT INTO int_db(id,name) VALUES(<database identifier>,'<source identifier>');
For example:
INSERT INTO int_db(id,name) VALUES(178,'InnateDB');
Re-running the Parser
If data files have already been parsed, but the development process dictates that they be parsed again, potentially to populate a test database, it is necessary to delete various files which are written to the filesystem by the parser in order to prevent repeated parsing of data. These files are called lastUpdate.obj and contain information about previous parsing operations.
find /home/irefindex/data -name lastUpdate.obj | xargs rm
Modifying Generated Data
New sources require changes to some generated data tables and to the programs that populate them:
- In the definition of the cy_edgeatrib_canonical table in the make_canonical_tables.sql file in the SQL_commands directory, a new column is required for each newly defined source.
- The src/process/no/uio/biotek/Make_Cy_tables.java file in BioPSI_Suplimenter needs to be changed so that the popCombine_edge method has a set of statements populating the new column created in the cy_edgeatrib_canonical table, and the src/process/no/uio/biotek/PreProcess_process.java file also needs changing so that the definition of the cy_edgeatrib table in the commit method includes a new column for each newly defined source.
- The make_iRefWeb.sql file in the SQL_commands directory requires a statement defining each new source in the source_db table.
All iRefIndex Pages
Follow this link for a listing of all iRefIndex related pages (archived and current).
