Textpresso DTD

<!-- TEXTPRESSO DTD, VERSION 3.1 --> <!-- Hans-Michael Muller & Eimear E. Kenny --> <!-- 08/09/2002 --> <!-- ******** DOCUMENT CONTENT MODEL******** --> <!-- Document is being parsed by Perl scripts: In each ELEMENT and --> <!-- ATTLIST line , leave comments as they are. --> <!-- ** document root tag ** --> <!ENTITY commasign "&#44;"> <!ENTITY colonsign "&#58;"> <!ENTITY roundbracket "&#40;"> <!ELEMENT article (sentence+)> <!--**document parent tag**--> <!ELEMENT sentence (organism | drugs | gene | clone | transgene | allele | strain | phenotype | sex | involvement | association | cnsort | regulation | effect | itention | localization |method | process | pathway | nmber | negation | pnoun | modality | auxiliary | cjunction | punctuation | pposition | determiner | mark | cell | life_stage | component | function | cmparison | spatial_relation | characterization | time_relation | entity_feature | nucleic_acid | bracket | action | dscriptor | mutants | text)*> <!ATTLIST sentence id ID #REQUIRED> <!-- ** document children tags ** --> <!-- # --> <!ELEMENT text (#PCDATA)> <!-- # --> <!ELEMENT action (#PCDATA)> <!-- action --> <!ATTLIST action grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!-- # --> <!ELEMENT allele (#PCDATA)> <!-- allele --> <!ATTLIST allele reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST allele grammar (FW | NN | NNS | NNP | NNPS | PDT | PRP | PRS | RBR | RBS | WDT | WP | WPS) #REQUIRED> <!-- # --> <!ELEMENT association (#PCDATA)> <!-- association --> <!ATTLIST association grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!-- # --> <!ELEMENT auxiliary (#PCDATA)> <!ATTLIST auxiliary grammar (VB | VBD | VBN | VBP | VBZ) #REQUIRED> <!ATTLIST auxiliary type (be | have) #IMPLIED> <!-- # --> <!ELEMENT bracket (#PCDATA)> <!ATTLIST bracket grammar (roundbracket | SYM) #REQUIRED> <!ATTLIST bracket type (so | sc | ro | rc) #IMPLIED> <!-- # --> <!ELEMENT cell (#PCDATA)> <!-- cell or cell group --> <!ATTLIST cell reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST cell grammar (FW | NN | NNS | NNP | NNPS | PDT | PRP |PRS | RBR | RBS | WDT | WP | WPS) #REQUIRED> <!ATTLIST cell type (name | lineage | group) #IMPLIED> <!-- (na-name | li-lineage | gr-group) cell or cell group type --> <!-- # --> <!ELEMENT characterization (#PCDATA)> <!-- characterization --> <!ATTLIST characterization grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!-- # --> <!ELEMENT cjunction (#PCDATA)> <!ATTLIST cjunction grammar (CC) #REQUIRED> <!ATTLIST cjunction type (coordinating | necessity | reasoning) #IMPLIED> <!-- # --> <!ELEMENT clone (#PCDATA)> <!-- clone --> <!ATTLIST clone reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST clone grammar (FW | NN | NNS | NNP | NNPS | PDT | PRP |PRS | RBR | RBS | WDT | WP | WPS) #REQUIRED> <!-- # --> <!ELEMENT cmparison (#PCDATA)> <!-- comparison --> <!ATTLIST cmparison grammar (RB | RBR | RBS | JJ | JJR | JJS | VB | VBD | VBG | VBN | VBP | VBZ | NN | NNS) #REQUIRED> <!ATTLIST cmparison type (similar | identical | different | unknown) #IMPLIED> <!-- (si-similar | id-identical | di-different) comparison type --> <!-- # --> <!ELEMENT cnsort (#PCDATA)> <!-- consort --> <!ATTLIST cnsort grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!ATTLIST cnsort type (positive | negative | unknown) #IMPLIED> <!-- (po-positive | ne-negative) consort type --> <!-- # --> <!ELEMENT component (#PCDATA)> <!-- cellular component --> <!ATTLIST component reference (direct | indirect ) #IMPLIED> <!ATTLIST component grammar (NN | NNS | NNP | NNPS) #REQUIRED> <!ATTLIST component source (go | textpresso) #IMPLIED> <!-- (go-go | te-textpresso) component source --> <!-- # --> <!ELEMENT determiner (#PCDATA)> <!ATTLIST determiner grammar (DT) #REQUIRED> <!-- # --> <!ELEMENT drugs (#PCDATA)> <!-- drugs --> <!ATTLIST drugs reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST drugs grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!ATTLIST drugs type (antibiotic | unknown) #IMPLIED> <!-- (an-antibiotic) drugs type --> <!-- # --> <!ELEMENT dscriptor (#PCDATA)> <!-- descriptor --> <!ATTLIST dscriptor grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!-- # --> <!ELEMENT effect (#PCDATA)> <!-- effect --> <!ATTLIST effect grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!ATTLIST effect type (positive | negative | unknown) #IMPLIED> <!-- (po-positive | ne-negative) effect type --> <!-- # --> <!ELEMENT entity_feature (#PCDATA)> <!-- entity feature --> <!ATTLIST entity_feature reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST entity_feature grammar (FW | NN | NNS | NNP | NNPS | PDT | PRP | PRS | RBR | RBS | WDT | WP | WPS) #REQUIRED> <!ATTLIST entity_feature type (protein | DNA | RNA | other) #IMPLIED> <!-- (pr-protein | DN-DNA | RN-RNA) entity feature type --> <!-- # --> <!ELEMENT function (#PCDATA)> <!-- molecular function --> <!ATTLIST function reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST function grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!ATTLIST function source (go | textpresso) #IMPLIED> <!-- (go-go | te-textpresso) molecular function source --> <!ATTLIST function protein (yes | no) #IMPLIED> <!-- (ye-yes | no-no) molecular function protein --> <!-- # --> <!ELEMENT gene (#PCDATA)> <!-- gene --> <!ATTLIST gene reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST gene grammar (FW | NN | NNS | NNP | NNPS | PDT | PRP |PRS | RBR | RBS | WDT | WP | WPS) #REQUIRED> <!-- # --> <!ELEMENT involvement (#PCDATA)> <!-- involvement --> <!ATTLIST involvement grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!ATTLIST involvement requirement (yes | no) #IMPLIED> <!-- (ye-yes | no-no) involvement requirement --> <!-- # --> <!ELEMENT itention (#PCDATA)> <!-- purpose --> <!ATTLIST itention grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!-- # --> <!ELEMENT life_stage (#PCDATA)> <!-- life stage --> <!ATTLIST life_stage reference (direct | indirect ) #IMPLIED> <!ATTLIST life_stage grammar (NN | NNS | NNP | NNPS) #REQUIRED> <!-- # --> <!ELEMENT localization (#PCDATA)> <!-- localization --> <!ATTLIST localization grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!ATTLIST localization type (spatial | temporal | general | unknown) #IMPLIED> <!-- (sp-spatial | te-temporal | ge-general) localization type --> <!-- # --> <!ELEMENT method (#PCDATA)> <!-- method --> <!ATTLIST method grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!-- # --> <!ELEMENT mark (#PCDATA)> <!ATTLIST mark grammar (JJ | RB) #REQUIRED> <!ATTLIST mark type (positive | negative | unknown) #IMPLIED> <!-- # --> <!ELEMENT modality (#PCDATA)> <!ATTLIST modality grammar (VBP | MD) #REQUIRED> <!-- # --> <!ELEMENT mutants (#PCDATA)> <!-- mutant --> <!ATTLIST mutants reference (direct | indirect ) #IMPLIED> <!ATTLIST mutants grammar (NN | NNS | NNP | NNPS) #REQUIRED> <!-- # --> <!ELEMENT negation (#PCDATA)> <!-- negation --> <!ATTLIST negation grammar (RB | RP | VB) #REQUIRED> <!-- # --> <!ELEMENT nmber (#PCDATA)> <!ATTLIST nmber grammar (CD) #REQUIRED> <!-- # --> <!ELEMENT nucleic_acid (#PCDATA)> <!-- nucleic acid --> <!ATTLIST nucleic_acid reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST nucleic_acid grammar (FW | NN | NNS | NNP | NNPS | PDT | PRP | PRS | RBR | RBS | WDT | WP | WPS) #REQUIRED> <!ATTLIST nucleic_acid type (DNA | RNA | other) #IMPLIED> <!-- (DN-DNA | RN-RNA) nucleic acid type --> <!-- # --> <!ELEMENT organism (#PCDATA)> <!-- organism --> <!ATTLIST organism reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST organism grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | WDT | WP | WPS) #REQUIRED> <!-- # --> <!ELEMENT pathway (#PCDATA)> <!-- pathway --> <!ATTLIST pathway grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | WDT | WP | WPS) #REQUIRED> <!ATTLIST pathway type (evolutionary | cellular | molecular | all) #IMPLIED> <!-- (ev-evolutionary | ce-cellular | mo-molecular | ge-general) pathway type --> <!ATTLIST pathway course (downstream | upstream | parallel | bypass | unknown) #IMPLIED> <!-- (do-downstram | up-upstream | pa-parallel | by-bypass) pathway course --> <!-- # --> <!ELEMENT phenotype (#PCDATA)> <!-- phenotype --> <!ATTLIST phenotype reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST phenotype grammar (FW | JJ | NN | NNP | NNS | NNPS | PDT | POS | PRP | PRS | RB | WDT) #REQUIRED> <!-- # --> <!ELEMENT pnoun (#PCDATA)> <!ATTLIST pnoun grammar (PRP | PRS | WDT) #REQUIRED> <!-- # --> <!ELEMENT pposition (#PCDATA)> <!ATTLIST pposition grammar (IN | TO) #REQUIRED> <!ATTLIST pposition type (with | by | between | through | of | in | on | to |because_of) #IMPLIED> <!-- # --> <!ELEMENT process (#PCDATA)> <!-- biological process --> <!ATTLIST process grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!ATTLIST process source (go | textpresso) #IMPLIED> <!-- (go-go | te-textpresso) process source --> <!ATTLIST process type (cellular | molecular | organismal | general) #IMPLIED> <!-- (ce-cellular | mo-molecular | or-organismal | ge-general) process type --> <!ATTLIST process biosynthesis (expression | tlation | tscription | replication | other | no) #IMPLIED> <!-- (ex-expression | tl-translation | ts-transcription | re-replication | ot-other | no-no) process biosynthesis --> <!-- # --> <!ELEMENT punctuation (#PCDATA)> <!ATTLIST punctuation grammar (colonsign | commasign) #REQUIRED> <!ATTLIST punctuation type (comma | semicolon | kolon | hyphen | fslash) #IMPLIED> <!-- # --> <!ELEMENT regulation (#PCDATA)> <!-- regulation --> <!ATTLIST regulation grammar (FW | JJ | JJR | JJS | NN | NNS | NNP | NNPS | PDT | PRP | RBR | RBS | VB | VBD | VBG | VBN | VBP | VBZ | WDT | WP | WPS) #REQUIRED> <!ATTLIST regulation type (positive | negative | unknown) #IMPLIED> <!-- (po-positive | ne-negative) regulation type --> <!-- # --> <!ELEMENT sex (#PCDATA)> <!-- sex --> <!ATTLIST sex reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST sex grammar (JJ | NN | NNS) #REQUIRED> <!ATTLIST sex type (male | female | hermaphrodite) #IMPLIED> <!-- (ma-male | fe-female | he-hermaphrodite) sex type --> <!-- # --> <!ELEMENT spatial_relation (#PCDATA)> <!-- spatial relation --> <!ATTLIST spatial_relation grammar (JJ | NN | NNS | RB) #REQUIRED> <!ATTLIST spatial_relation type (close | distant | unknown) #IMPLIED> <!-- (cl-close | di-distant) spatial relation type --> <!-- # --> <!ELEMENT strain (#PCDATA)> <!-- strain --> <!ATTLIST strain reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST strain grammar (FW | NN | NNS | NNP | NNPS | PDT | PRP | PRS | RBR | RBS | WDT | WP | WPS) #REQUIRED> <!-- # --> <!ELEMENT time_relation (#PCDATA)> <!-- time relation --> <!ATTLIST time_relation grammar (JJ | NN | NNS | RB) #REQUIRED> <!ATTLIST time_relation type (earlier | later | simultaneously |unknown) #IMPLIED> <!-- (ea-earlier | la-later | si-simultaneously) time relation type --> <!-- # --> <!ELEMENT transgene (#PCDATA)> <!-- transgene --> <!ATTLIST transgene reference (direct | indirect | unknown) #IMPLIED> <!ATTLIST transgene grammar (FW | NN | NNS | NNP | NNPS | PDT | PRP | PRS | RBR | RBS | WDT | WP | WPS) #REQUIRED>