PepcDB Schema Content
Content and Report Formats:
|
Definitions of the various terms within the PepcDB schema
pepcDB Schema version
Format version identifier (i.e. 6,7,8,9 or 9.1), the current version is 9.1
XML Presentation:
<pepcFormatVersion>9.1</pepcFormatVersion>back to top
To search targets from a single Structural Genomics center, select one of the project sites from the list below.
The PSI Structural Genomics Centers:
- Berkeley Structural Genomics Center (BCSG)
- Joint Center for Structural Genomics (JCSG)
- Midwest Center for Structural Genomics (MCSG)
- Northeast Structural Genomics Consortium (NESG)
- New York SGX Research Center for Structural Genomics (NYSGXRC)
- Southeast Collaboratory for Structural Genomics (SECSG)
- TB Structural Genomics Consortium (TB)
- Center for Eukaryotic Structural Genomics (CESG)
- Structural Genomics for Pathogenic Protozoa (SGPP)
Other Projects:
- Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
- Structure 2 Function Project (S2F)
Asia:
Europe:
- Paris-Sud Yeast Structural Genomics (YSG)
- Marseilles Structural Genomics Program @ AFMB (MSGP)
- Bacterial targets at IGS-CNRS, France (BIGS)
- Oxford Protein Production Facility (OPPF)
- Structural Proteomics in Europe (SPINE)
- German Mycobacterium Tuberculosis Structural Genomics Consortium (XMTB)
XML Presentation:
<site>TB</site>back to top
Contact Information List
All contact information related to this target, target collection, or related experimental trials is listed here and referenced later.
XML Presentation:
<contactInfoList>
<contactInfo>
<contactInfoId>c_1</contactInfoId>
<name>TB Consortium - Database Group</name>
<address>Room 105, MBI, Los Angeles 90095</address>
<country>USA</country>
<email>tbdbteam@mbi.ucla.edu</email>
<organization>TB Structural Genomics Consortium</organization>
<lab>Laboratory of David Eisenberg</lab>
<role>Archiver</role>
</contactInfo>
<contactInfo>
<contactInfoId>c_2</contactInfoId>
<name>LANL-Protein Production Facility</name>
<address>Los Alamos, NM 87545</address>
<country>USA</country>
<email>ppteam@lanl.gov</email>
<organization>Los Alamos National Laboratory</organization>
<lab>Los Alamos National Laboratory</lab>
<role>Scientist;/role>
</contactInfo>
</contactInfoList>
back to topContact information ID
An identifier for contact information related to a particular target. The identifier is defined by each structural genomics center.
Examples:
- c_1
- c_2
<contactInfoId>c_2</contactInfoId>back to top
Name
Name of a group, division, or individual researcher who contributed to the target structural analysis.
Examples:
- TB Consortium - Database Group
- LANL-Protein Production Facility
<name>TB Consortium - Database Group</name>back to top
Address
Detailed address of a group, division, or individual researcher who contributed to the target structural analysis.
Examples:
- Room 105, MBI, Los Angeles 90095
- Los Alamos, NM 87545
<address>Room 105, MBI, Los Angeles 90095</address>back to top
Examples:
- United States = US
- United Kingdom = GB
<country>US</country>back to top
Examples:
- target-help@rcsb.rutgers.edu
<email>target-help@rcsb.rutgers.edu</email>back to top
Examples:
- TB Structural Genomics Consortium
<organization>TB Structural Genomics Consortium</organization>back to top
Examples:
- Laboratory of David Eisenberg
- Los Alamos National Laboratory
XML Presentation:
<lab>Laboratory of David Eisenberg</lab>back to top
Role
Text description of the role of the group or individual for which contact information is provided
Examples:
- Archiver
- Scientist
XML Presentation:
<role>Archiver</role>back to top
Protocol List
A reusable list of protocols which must include a unique
identifier and a text section describing the protocol. The protocol
identifier may be any simple code (e.g. 1, 2, clone1, pur_1, etc). The
protocol definition may also optionally include a name and a brief
description.
The protocols defined in this list are referenced in
describing the experimental trials attempted on each target.
XML Presentation:
<protocolList>
<protocol>
<protocolId>pur_1</protocolId>
<protocolName>Gel filtration 1</protocolName>
<protocolDescription>
Gel filtration purification by FPLC from Pharmacia.
<protocolDescription/>
<protocolText>
Protocol text...
</protocolText>
</protocol>
<protocol>
<protocolId>pur_2</protocolId>
<protocolName>Cation exchange chromatography 2</protocolName>
<protocolDescription>
Cation exchange purification by FPLC from Pharmacia.
<protocolDescription/>
<protocolText>
Protocol text...
</protocolText>
</protocol>
</protocolList>
back to topProtocol ID
A unique protocol identifier is any simple code defined by a Structural Genomics Center.
Examples:
- clone1
- pur_1
XML Presentation:
<protocolId>pur_1</protocolId>back to top
Protocol Name
The protocol name defined by the Structural Genomics Center.
Examples:
- Gel filtration 1
- Cloning
XML Presentation:
<protocolName>Gel filtration 1</protocolName>back to top
Protocol Description
A brief description of a protocol.
Examples:
- Gel filtration by FPLC from Pharmacia
- Cloning into pET expression vector from Stratagene
XML Presentation:
<protocolDescription>Gel filtration by FPLC from Pharmacia</protocolDescription>back to top
Protocol Text
A detailed description of a protocol.
Examples:
XML Presentation:
<protocolText>Protocol text..</protocolText>back to top
Project Target List
A description of a project target including a list of trials used to produce the protein and solve the structure.
back to top
Project pepcTarget ID
A unique identifier for a project target sequence defined by each structural genomics center, but it must be unique within the project target list and consistent across target list updates.
Examples:
- WR90EC
- NYSGRC-P007
XML Presentation:
<id>WR90EC</id>back to top
PSI Project List
List of of SG projects/programs with which target is associated. For example: PSI (Protein Structure Initiative), phase one or phase two.
XML Presentation:
<projectList>
<project>
<projectName>PSI</projectName>
<projectId>1</projectId>
</project>
<project>
<projectName>PSI</projectName>
<projectId>2</projectId>
</project>
</projectList>
back to
topProgram Name
Abbreviated name of Structural Genomics project. Example: PSI (Protein Structure Initiative)
Examples:
- PSI
<projectName>PSI</projectName>back to top
Project ID
Project identifier. Example: 1 or 2 to identify Protein Structure Initiative(PSI)
first or second research phase.
Examples:
- 1
- 2
<projectId>2</projectId>back to top
Target Category List
Information about target being
assosiated with a specific category of targets such as targets
that have biomedical significance or targets that are nominated
by scientific community.
<targetCategoryList>
<targetCategory>
<targetCategoryName>biomedical</targetCategoryName>
<remark>any comments about biomedical significance
of this target</remark>
</targetCategory>
<targetCategory>
<targetCategoryName>community nominated</targetCategoryName>
<remark>information about the nominator such as
name and affiliation</remark>
</targetCategory>
</targetCategoryList>
back to
topTarget Category Name
Name of target category from enumerated list of defined target categories.
- biomedical
- community nominated
- metagenomic
- membrane protein
- legacy
- structural coverage
<targetCategoryName>biomedical</targetCategoryName>back to top
Target Category Remark
Any additional information related to target being in this
particular category. For example, what is target biomedical significance
or inforamtion about a person who nominated this target such as
name and affiliation.
- Studies suggest that this protein is involved in lung cancer.
<reamrk>
Studies suggest that this protein is involved in lung cancer.
</remark>
back to
topTarget Current Status
The current status of this target from PepcDB defined status codes.
<status>NMR assigned</status>back to top
Target Stop Details
Information describing the details for
stopping work on this target.
This includes a code from an enumerated list describing the stage
at which work on target was stopped and any additional details.
<targetStopDetails>
<stopStatus>crystallization failed</stopStatus>
<remark>possible explanation of crystalization failure</remark>
</targetStopDetails>
back to
topTarget Stop Status
The status code describing the stage of work at which this target was terminated.
- expression failed
- cloning failed
- purification failed
- crystallization failed
- poor diffraction
- poor NMR
- duplicate target found
- internal duplicate found
- TargetDB duplicate found
- PDB duplicate found
- mass spec failed
- sequencing failed
- structure successful
- other
<stopStatus>expression failed</stopStatus>back to top
Target Stop Remark
An optional remark explaining the reason of stopping the work on a target
<reamrk>
Degradation of the expressed product
</remark>
back to
topRelated Target ID List
The list of target IDs that are related to the project
target.
<relatedTargetIdList>
<relatedTargetId>
<id>TX1001</id>
<remark>a similar sequence in mouse</remark>
</relatedTargetId>
<relatedTargetId>
<id>TX900</id>
<remark>a similar sequence in rat</remark>
</relatedTargetId>
</relatedTargetIdList>
back to topRelated Target ID
A unique identifier for a target related to the project target.
- TX1001
<id>TX1001</id>back to top
Related Target Remark
Description of the relationship of project target and related target.
- a similar sequence in mouse
<remark>a similar sequence in mouse</remark>back to top
Sequence List
A packet of information describing sequences related to target.
Sequences are described by a one-letter code sequence, by type
(i.e. protein, clone, subclone, etc), chemical type (i.e. protein
or dna) and construct type (i.e. full orf, domain, fragment, etc.).
In defining a target sequence, it is assumed that the sequence will correspond
most closely with the sequence of the ultimate
structure determination.
<targetSequenceList>
<targetSequence>
<oneLetterCode>
MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
</oneLetterCode>
<sequenceType>protein</sequenceType>
<sequenceChemicalType>protein</sequenceChemicalType>
<sequenceConstructType>domain</sequenceConstructType>
</targetSequence>
<targetSequence>
<oneLetterCode>
MLKVNNLSKIWKDFKLKNVSFEIDREYCVILGPSGAGKSVLIKCIAGILKPDSGRIIL
</oneLetterCode>
<sequenceType>protein</sequenceType>
<sequenceChemicalType>protein</sequenceChemicalType>
<sequenceConstructType>domain</sequenceConstructType>
</targetSequence>
</targetSequenceList>
back to topSequence Code
The one-letter code sequence for FASTA comparison.
Examples:
MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
XML Presentation:
<oneLetterCode>
MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
</oneLetterCode>
back to topSequence Type
The type of sequence specified.
Examples:
- protein
- experimental protein
- predicted dna
- clone
- subclone
- predicted protein
<sequenceType>protein</sequenceType>back to top
Sequence Chemical Type
Chemical classification of sequence data.
Examples:
- protein
- dna
<sequenceChemicalType>protein</sequenceChemicalType>back to top
Sequence Construct Type
The construct type for this sequence.
Examples:
- full ORF
- domain
- fragment
<sequenceConstructType>full ORF</sequenceConstructType>back to top
Protein Name
The name of the protein for the target sequence.
Examples:
- Glutamate synthase
- 29-C10
<proteinName>Glutamate synthase</proteinName>back to top
Target URL
Universal resource locator/internet address related to this
target. This can be a link to a project site containing more
information about
this target, or some other related site address.
Example:
- http://www.doe-mbi.ucla.edu/TB/PUBLIC/qs/qsearch.php?dowork=Rv2031c
<url>http://www.doe-mbi.ucla.edu/TB/PUBLIC/qs/qsearch.php?dowork=Rv2031c</url>back to top
Remark
Additional text details about this target.
Example:
- A remarkably insightful comment about this target.
<remark>A remarkably insightful comment about this target.</remark>back to top
Source Organism
The scientific name of the source organism for the target
sequence following the nomenclature of the NCBI Taxonomy database
(http://www.ncbi.nih.gov/Taxonomy).
Examples:
- Mycobacterium tuberculosis
- Arabidopsis thaliana
- Escherichia coli
- Caenorhabditis elegans
<sourceOrganism>Mycobacterium tuberculosis</sourceOrganism>back to top
Database List
A list describing related information about this target including a database name and an identifier within the database.
XML Presentation:
<databaseRefList>
<databaseRef>
<databaseName>TB.proteomic_information</databaseName>
<databaseId>367989</databaseId>
</databaseRef>
<databaseRef>
<databaseName>Genbank</databaseName>
<databaseId>189676547</databaseId>
</databaseRef>
<databaseRef>
<databaseName>PDB</databaseName>
<databaseId>1A2B</databaseId>
</databaseRef>
</databaseRefList>
back to topDatabase Name
The database name
Examples:
- TB.proteomic_information
- Genbank
- PDB
<databaseName>TB.proteomic_information</databaseName>back to top
Database ID
The accession code for the named database
Examples:
- 367989
- 189676547
- 1A2B
<databaseId>367989</databaseId>back to top
Contact Information Reference List
A list of contacts responsible for this target identified
by referencing the previously defined contact information list
XML Presentation:
<contactInfoRefList>
<contactInfoRef>
<contactInfoId>c_1</contactInfoId>
</contactInfoRef>
<contactInfoRef>
<contactInfoId>c_2</contactInfoId>
</contactInfoRef>
</contactInfoRefList>
back to topContact Information ID
References previously defined contact IDs from Contact Information List.
Examples:
- c_1
- c_2
<contactInfoId>c_1</contactInfoId>back to top
Trial List
A list of protein production trials attempted for this target. This should
include both successful and failed trials.
Each trial consists of a description of a set of the sequence tasks employed
to produce this target. A trial includes: lab, date, contact information,
experimental sequence data, process status data, and references to the
protocols used in the trial.
XML Presentation:
<trialList>
<trial>
<trialId>...</trialId>
<cloneId>...</cloneId>
<lab>...</lab>
<date>...</date>
<contactInfoRefList>
<!-- List of Contact References -->
</contactInfoRefList>
<status>....</status>
<statusHistoryList>
<!-- Status History List -->
</statusHistoryList>
<trialSequenceList>
<!-- List of Trial Sequences -->
</trialSequenceList>
<trialProtocolList>
<!-- List of Trial Protocols -->
</trialProtocolList>
</trial>
<trial>
<lab>...</lab>
<date>...</date>
<contactInfoRefList>
<!-- List of Contact References -->
</contactInfoRefList>
<status>....</status>
<statusHistoryList>
<!-- Status History List -->
</statusHistoryList>
<trialSequenceList>
<!-- List of Trial Sequences -->
</trialSequenceList>
<trialProtocolList>
<!-- List of Trial Protocols -->
</trialProtocolList>
</trial>
</trialList>
back to
topTrial ID
Optional trial ID defined by structural genomics center
Example:
- 12345a1BCt1p1_54321_1_63421
<trialId>12345a1BCt1p1_54321_1_63421</trailId>back to top
Material Repository Clone ID
Optional clone ID from
PlasmID database. Provide clone ID if a clone (vector plus DNA insert)
associated with this experimental trial was deposited to PSI Material
Repository.
Example:
- 83561
<cloneId>83561</cloneId>back to top
Date
Date on which this trial information was updated - yyyy-mm-dd.
Example:
- 2001-02-14
<date>2001-02-14</date>back to top
Trial Contact Information List
A list of contacts responsible for this trial identified
by referencing the previously defined contact information list.
XML Presentation:
<contactInfoRefList>
<contactInfoRef>
<contactInfoId>c_1</contactInfoId>
</contactInfoRef>
<contactInfoRef>
<contactInfoId>c_2</contactInfoId>
</contactInfoRef>
</contactInfoRefList>
back to
topTrial Contact Information ID
References previously defined contact IDs from Contact Information List.
Examples:
- c_1
- c_2
<contactInfoId>c_1</contactInfoId>back to top
Status
The current status of this trial. This should correspond to
the last status recoreded in the status history list.
Examples:
- selected
- cloned
- expressed
- soluble
- purified
- mass spec verified
- crystallized
- diffraction-quality crystals
- diffraction
- native diffraction-data
- phasing diffraction-data
- HSQC
- NMR assigned
- crystal structure
- NMR structure
- in BMRB
- in PDB
- work stopped
- test target
- other
<status>selected</status>back to top
Status History List
List of timestamped codes describing critical changes in target status.
The status history record includes laboratory name responsible for this trial,
an enumerated status state,
the date corresponding to the beginning of this status state,
and an optional completion date and remark.
XML Presentation:
<statusHistoryList>
<statusHistory>
<lab>Laboratory of David Eisenberg</lab>
<status>selected</status>
<date>2001-01-10</date>
<remark>optional remark</remark>
<dateComplete>2001-02-14</dateComplete>
<protocolId>sel_1</protocolId>
</statusHistory>
<statusHistory>
<lab>Laboratory of David Eisenberg</lab>
<status>cloned</status>
<date>2001-02-14</date>
<remark>optional remark</remark>
<dateComplete>2001-02-16</dateComplete>
<protocolId>clon_1</protocolId>
</statusHistory>
<statusHistory>
<lab>Laboratory of David Eisenberg</lab>
<status>expressed</status>
<date>2001-02-16</date>
<remark>optional remark</remark>
<dateComplete>2001-02-24</dateComplete>
<protocolId>expr_1</protocolId>
</statusHistory>
<statusHistory>
<lab>Laboratory of David Eisenberg</lab>
<status>soluble</status>
<date>2001-02-24</date>
<remark>optional remark</remark>
<dateComplete>2001-03-01</dateComplete>
</statusHistory>
<statusHistory>
<lab>Laboratory of David Eisenberg</lab>
<status>purified</status>
<date>2001-03-01</date>
</statusHistory><remark>optional remark</remark>
<dateComplete>2001-03-10</dateComplete>
<protocolId>pur_1</protocolId>
</statusHistory>
</statusHistoryList>
back to topTrial Laboratory Name
Name of laboratory responsible for this trial.
Examples:
- Laboratory of David Eisenberg
- Los Alamos National Laboratory
<lab>Laboratory of David Eisenberg</lab>back to top
Status
Status of a trial associated with a specific date
Examples:
- selected
- cloned
- expressed
- soluble
- purified
- mass spec verified
- crystallized
- diffraction-quality crystals
- diffraction
- native diffraction-data
- phasing diffraction-data
- HSQC
- NMR assigned
- crystal structure
- NMR structure
- in BMRB
- in PDB
- work stopped
- test target
- other
<status>selected</status>back to top
Status Date
Date of status of a trial
Example:
- 2001-02-14
<date>2001-02-14</date>back to top
Status Remark
An optional remark about status history of a trial
XML Presentation:
<remark>optional remark</remark>back to top
Status Completion Date
An optional completion date of a trial.
Example:
- 2001-02-14
<dateComplete>2001-02-14</dateComplete>back to top
Stop Details
Information describing the details for stopping work on this
trial. This includes a code from an enumerated list describing the stage
at which the trial was stopped and any additional details.
XML Presentation:
<stopDetails>
<stopStatus>expression failed</stopStatus>
<remark>Degradation of the expressed product</remark>
</stopDetails>
back to topStop Status
The status code describing the stage of work at which this trial was terminated.
Examples:
- expression failed
- cloning failed
- purification failed
- crystallization failed
- poor diffraction
- poor NMR
- duplicate target found
- internal duplicate found
- TargetDB duplicate found
- PDB duplicate found
- mass spec failed
- sequencing failed
- structure successful
- other
<stopStatus>expression failed</stopStatus>back to top
Stop Remark
An optional remark explaining the reason of stopping the work on a trial
Examples:
XML Presentation:
<remark>Degradation of the expressed product</remark>back to top
Trial Database List
A list describing related information about this trial sequence
including a database name and an identifier within the database.
In the situation when a target is associated with multiple PDB IDs
(structures of individual domains, structures with different
ligands) this data element can be used to present PDB ID associated
with a specific crystallization or NMR experimental trial.
Please note that trial database infromation should be also
referenced in the Target Database Reference List
XML Presentation:
<databaseRefList>
<databaseRef>
<databaseName>PDB</databaseName>
<databaseId>1A2B</databaseId>
</databaseRef>
</databaseRefList>
back to topDatabase Name
The database name
Examples:
- PDB
<databaseName>PDB</databaseName>back to top
Database ID
The accession code for the named database
Examples:
- 1A2B
<databaseId>1A2B</databaseId>back to top
Trial Sequence List
The list of experimental sequences related to this trial.
These may contain deliberate modifications or unanticipated
differences from the parent target protein sequence.
XML Presentation:
<trialSequenceList>
<trialSequence>
<oneLetterCode>
MATTLPPQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
</oneLetterCode>
<sequenceChemicalType>protein</sequenceChemicalType>
<sequenceModifications>valine 7 replaced by proline</sequenceModifications>
<sequenceDetails>five terminal residues cleaved</sequenceDetails>
</trialSequence>
<trialSequence>
<oneLetterCode>
MLKVNNLSKIWKDFKLKNVSFEIDREYCVILGPSGAGKSVLIKCIAGILKPDSGRIIL
</oneLetterCode>
<sequenceChemicalType>protein</sequenceChemicalType>
<sequenceModifications>valine 7 replaced by leucine</sequenceModifications>
<sequenceDetails>five terminal residues cleaved</sequenceDetails>
</trialSequence>
</trialSequenceList>
back to topTrial Sequence Code
The one-letter code sequence of a trial
Example:
MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
XML Presentation:
<oneLetterCode>
MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
</oneLetterCode>
back to topTrial Sequence Chemical Type
Chemical classification of trial sequence data.
Example:
- protein
- dna
<sequenceChemicalType>protein</sequenceChemicalType>
back to topTrial Construct Type
The construct type for this trial sequence.
Example:
- full ORF
- domain
- fragment
<sequenceConstructType>fragment</sequenceConstructType>
back to topTrial Sequence Modifications
Deliberate modifications or other unanticipated changes that may occur in a trial sequence
relative to the parent target sequence.
Example:
- valine 7 replaced by proline
<sequenceModifications>valine 7 replaced by proline</sequenceModifications>back to top
Trial Sequence Details
Changes that may occur in a trial sequence
relative to the parent target sequence.
Example:
- five terminal residues cleaved
<sequenceDetails>five terminal residues cleaved</sequenceDetails>back to top
Trial Protocol List
A list of references to protocols defined in the protocol
list that describe the tasks applied in this experimental trial.
Each protocol refers to a predefined protocol description
and can be accompanied by a type and optional additional details or
customization. Protocols are referenced by their protocolId
as previously defined in the protocol list.
XML Presentation:
<trialProtocolList>
<protocolRef>
<protocolId>pur_1</protocolId>
<protocolType>purification</protocolType>
<protocolDetails>
A cat wisker was added for good luck.
</protocolDetails>
</protocolRef>
<protocolRef>
<protocolId>pur_2</protocolId>
<protocolType>purification</protocolType>
<protocolDetails>
change in sodium chloride gradient range.
</protocolDetails>
</protocolRef>
</trialProtocolList>
back to topTrial Protocol ID
A reference to a predefined protocol ID from Protocol List.
Examples:
- clone1
- pur_1
<protocolId>pur_1</protocolId>back to top
Trial Protocol Type
Type of procedure descibed in the protocol
Examples:
- selection
- gene synthesis
- growth
- PCR
- cloning
- expression
- purification
- crystallization
- NMR
<protocolType>purification</protocolType>back to top
Trial Protocol Details
Changes that were intoduced into the main protocol which are specific to this trial.
Examples:
- cloning into different expression vector.
- change in expression time and/or temperature.
<protocolDetails>cloning into different expression vector..</protocolDetails>back to top
Trial Measurement List
List of measurements associated with this trial. This includes
name of a procedure which is used to collect the measurements,
collected measurements, reference to a protocol, and optional
details related to the measurements.
XML Presentation:
<trialMeasurementList>
<trialMeasurement>
<measurementProcedure>gel filtration</measurementProcedure>
<measurementList>
<measurement>
<measurementValue>300.00</measurementValue>
<measurementName>molecular weight</measurementName>
<measurementUnit>kDa</measurementUnit>
<measurementUncertainty>+/- 2.65</measurementUncertainty>
</measurement>
</measurementList>
<protocolId>Pur_1</protocolId>
<remark>Any important comments about this
measurement</remark>
</trialMeasurement>
<trialMeasurement>
<measurementProcedure>Mass spec</measurementProcedure>
<measurementList>
<measurement>
<measurementValue>S157</measurementValue>
<measurementName>phosphorylation</measurementName>
<measurementUnit></measurementUnit>
<measurementUncertainty></measurementUncertainty>
</measurement>
<measurement>
<measurementValue>K52</measurementValue>
<measurementName>methylation</measurementName>
<measurementUnit></measurementUnit>
<measurementUncertainty></measurementUncertainty>
</measurement>
</measurementList>
<protocolId>MassSpecAnalysis_2</protocolId>
<remark>Any important comments about this measurement</remark>
</trialMeasurement>
<trialMeasurement>
<measurementProcedure>X-ray fluorescence</measurementProcedure>
<measurementList>
<measurement>
<measurementValue>Magnesium</measurementValue>
<measurementName>element analysis</measurementName>
<measurementUnit></measurementUnit>
<measurementUncertainty></measurementUncertainty>
</measurement>
<measurement>
<measurementValue>1.05:1</measurementValue>
<measurementName>stoichiometry</measurementName>
<measurementUnit></measurementUnit>
<measurementUncertainty></measurementUncertainty>
</measurement>
<protocolId></protocolId>
<remark>Any important comments about this measurement</remark>
</trialMeasurement>
<trialMeasurement>
<measurementProcedure>isoelectric focusing</measurementProcedure>
<measurementList>
<measurement>
<measurementValue>6.5</measurementValue>
<measurementName>Isoelectric point</measurementName>
<measurementUnit></measurementUnit>
<measurementUncertainty>+/- 0.65</measurementUncertainty>
</measurement>
</measurementList>
<protocolId>2Dgel_1</protocolId>
<remark>Any important comments about this measurement</remark>
</trialMeasurement>
</trialMeasurementList>
back to
topTrial Measurement Procedure
Name of an experimental procedure used to collect measurement(s)
for this trial.
Examples:
- Mass spec analysis
- Gel filtration
- X-ray fluorescence
- Isoelectic focusing
<measurementProcedure>Gel filtration</measurementProcedure>back to top
Measurement List
List of measurements collected by this procedure. This includes
name of a measurement, measurement value, unit of measurement, and
measurement uncertainty.
XML Presentation:
<measurementList>
<measurement>
<measurementValue>Magnesium</measurementValue>
<measurementName>element analysis</measurementName>
<measurementUnit></measurementUnit>
<measurementUncertainty></measurementUncertainty>
</measurement>
<measurement>
<measurementValue>1.05:1</measurementValue>
<measurementName>magnesuim stoichiometry</measurementName>
<measurementUnit></measurementUnit>
<measurementUncertainty></measurementUncertainty>
</measurement>
</measurementList>
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topMeasurement Name
Name of measurement.
Examples:
- molecular weight
- isoelectric point
- phosphorylation
- methylation
- element analysis
- stoichiometry
<measurementName>isoelectric point<measurementName/>back to top
Measurement Value
Value of measurement
Examples:
- 300.00
- 6.5
- S157
- K50
- magnesium
- 1.05:1
<measurementValue>magnesium<measurementValue/>back to top
Measurement Unit
Unit of performed measurement if aplicable.
Examples:
- kDa
- um
<measurementUnit>kDa<measurementUnit/>back to top
Measurement Uncertainty
Uncertainty of performed measurement if aplicable.
Examples:
- +/-0.06
<measurementUncertainty>+/-0.06<measurementUncertainty/>back to top
FASTA Sequence Comparison Details
Pearson, W.R. and Lipman, D.J. Improved tools for biological sequence comparison. PNAS 85:2444-2448(1988)
The E()-value cutoff limits the number of scores and alignments
shown based on the expected number of scores. A cutoff value of
2.0 (-E 2.0) will show all library sequences with scores with an
expectation value <= 2.0.
For protein searches, matched sequences with E()-values < 0.01
for searches of 10,000 protein sequences are almost always
homologous. Frequently sequences with E()-values from 1 - 10 are
related as well. However, E()-values also reflect differences
between the amino acid composition of the query sequence and
that of the "average" database sequence. Thus, when
searches are done with query sequences with "biased"
amino-acid composition, unrelated sequences may have
"significant" scores because of sequence bias.
FASTA is available from ftp://ftp.virginia.edu/pub/fasta/.
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Report Formats
FASTA Format
Sequences of selected targets are output in Pearson/FASTA format.
Example:
>001| Protein Kinase (E.C.2.7.1.37) (cAPK) (Catalytic Subunit) GNAAAAKKGSEQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYA MKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFSE PHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEII LSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKR FGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEFback to top
XML Format
Features of selected PepcDB entry output in XML format.