protein_dna_binding_ident_micro.xml

<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="protein_dna_binding_ident_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="protein-DNA binding site identification" term-accession="" source-abbreviation=""/><technology term-label="DNA microarray" term-accession="http://purl.obolibrary.org/obo/OBI_0400148" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]
            </generated-value-template></field><protocol-field protocol-type ="nucleic acid preparation"/><field header="Parameter Value[cross linking]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[a protocol parameter specific to Chromatin immuprecipitation in this context]]></description><default-value><![CDATA[]]></default-value><list-values>uv-light,formaldehyde,di-tert-butyl peroxide,formaldehyde and di-tert-butyl peroxyde</list-values></field><field header="Parameter Value[DNA fragmentation]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[a parameter value to report the method used for shearing DNA. Classic methods are sonication, nebulisation]]></description><default-value><![CDATA[]]></default-value><list-values>sonication,nebulization,micrococcal nuclease digestion,deoxyribonuclease digestion</list-values></field><field header="Parameter Value[DNA fragment size]" data-type="Double" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[a parameter to report the intended DNA fragment size resulting from the DNA fragmentation process (aka DNA shearing)]]></description><default-value><![CDATA[]]></default-value></field><unit-field data-type="Ontology term" is-multiple-value="false" is-required="false" is-forced-ontology="false"><description>unit to express nucleic acid size"</description></unit-field><field header="Parameter Value[immunoprecipitation antibody]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[a parameter to report immunoprecipitation antibody details. Structure information as follows: antibody name;antibody manufacturer;antibody catalog number;antibody dilution factor;clonality]]></description><default-value><![CDATA[]]></default-value></field><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>
                [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]
            </generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Identifier for the labeled extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>
                [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]
            </generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Indicates a chemical or biological marker, such as a radioactive isotope or a fluorescent dye which is bound to a material in order to make it detectable by some assay technology (e.g. P33, biotin, GFP).]]></description><default-value></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="49736"/></recommended-ontologies></field><protocol-field protocol-type ="nucleic acid hybridization"/><field header="Hybridization Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>
                [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].HYB-[HYB_COUNT]
            </generated-value-template></field><field header="Array Design REF" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Reference to the identifier (or accession number) of an existing array design]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[ARRAY_DESIGN]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Scan Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[User-defined name for each scan event.]]></description><default-value><![CDATA[]]></default-value></field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Name (or URI) of the image files generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="normalization data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="true" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Name (or URI) of the raw array data matrix file.]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="true" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Name (or URI) of the processed data matrix file resulting from data transformation or processing.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="factors"/></isatab-configuration></isatab-config-file>