<!-- Document type definition for proteome database --> <!-- Human Proteome Markup Language(HUP-ML) hup-ml.dtd --> <!-- Version 0.80 Aug. 25, 2003 NEC --> <!ELEMENT proteome (gel*)> <!ATTLIST proteome label CDATA #REQUIRED dtd_version CDATA #REQUIRED > <!ELEMENT gel (submitter?, source_info?, sample_preparation?, gel_conditions?, marker_protein?, detection?, gel_image_info?, spot_recognition?, spot_list?, comment?)> <!ATTLIST gel label CDATA #REQUIRED type CDATA #REQUIRED accession CDATA #REQUIRED > <!ELEMENT submitter (person+)> <!ELEMENT person (name, affiliation?, title?, email?, phone?, fax?)> <!ATTLIST person person_id CDATA #IMPLIED created_date CDATA #IMPLIED modified_date CDATA #IMPLIED > <!ELEMENT name (#PCDATA)> <!ELEMENT affiliation (#PCDATA)> <!ELEMENT title (#PCDATA)> <!ELEMENT email (#PCDATA)> <!ELEMENT phone (#PCDATA)> <!ELEMENT fax (#PCDATA)> <!ELEMENT source_info (source?, common_name?, strain?, cultivar?, cell_line?, organ?, tissue?, subcellular_fraction?, organella?, body_fluid?, excretion?, growth_phase?, comment?)> <!ATTLIST source_info source_info_id CDATA #IMPLIED created_date CDATA #IMPLIED modified_date CDATA #IMPLIED > <!ELEMENT source (#PCDATA)> <!ELEMENT common_name (#PCDATA)> <!ELEMENT strain (#PCDATA)> <!ELEMENT cultivar (#PCDATA)> <!ELEMENT cell_line (#PCDATA)> <!ELEMENT organ (#PCDATA)> <!ELEMENT tissue (#PCDATA)> <!ELEMENT subcellular_fraction (#PCDATA)> <!ELEMENT organella (#PCDATA)> <!ELEMENT body_fluid (#PCDATA)> <!ELEMENT excretion (#PCDATA)> <!ELEMENT growth_phase (#PCDATA)> <!ATTLIST growth_phase unit CDATA #IMPLIED > <!ELEMENT sample_preparation (tissue_disruption?, extraction?, protease_inhibitor*, conc?, other_materials?, solution*)> <!ATTLIST sample_preparation sample_preparation_id CDATA #IMPLIED created_date CDATA #IMPLIED modified_date CDATA #IMPLIED > <!ELEMENT tissue_disruption (#PCDATA)> <!ELEMENT extraction (procedure, comment?)> <!ELEMENT procedure (process+)> <!ELEMENT process ((add_solution | add_solvent | gravity | extraction_with)?, repetition?, comment?)> <!ATTLIST process seq CDATA #REQUIRED action CDATA #REQUIRED collection CDATA #IMPLIED time CDATA #IMPLIED time_unit CDATA #IMPLIED temperature CDATA #IMPLIED temperature_unit CDATA #IMPLIED > <!ELEMENT add_solution (#PCDATA)> <!ATTLIST add_solution solution_id CDATA #IMPLIED solution_volume CDATA #IMPLIED solution_unit CDATA #IMPLIED > <!ELEMENT gravity (#PCDATA)> <!ELEMENT extraction_with (#PCDATA)> <!ATTLIST extraction_with solvent CDATA #IMPLIED > <!ELEMENT repetition (#PCDATA)> <!ATTLIST repetition times CDATA #IMPLIED > <!ELEMENT add_solvent (#PCDATA)> <!ATTLIST add_solvent final_conc CDATA #IMPLIED unit CDATA #IMPLIED name CDATA #IMPLIED > <!ELEMENT protease_inhibitor (item_protease_inhibitor+, comment?)> <!ATTLIST protease_inhibitor id CDATA #IMPLIED label CDATA #IMPLIED > <!ELEMENT item_protease_inhibitor EMPTY> <!ATTLIST item_protease_inhibitor conc CDATA #IMPLIED unit CDATA #IMPLIED name CDATA #IMPLIED > <!ELEMENT conc (procedure, comment?)> <!ELEMENT other_materials (item_other_materials+)> <!ELEMENT item_other_materials (comment?)> <!ATTLIST item_other_materials name CDATA #IMPLIED size CDATA #IMPLIED size_unit CDATA #IMPLIED > <!ELEMENT solution (item_solution+, solvent?, comment?)> <!ATTLIST solution solution_id CDATA #IMPLIED label CDATA #IMPLIED > <!ELEMENT item_solution (#PCDATA)> <!ATTLIST item_solution conc CDATA #IMPLIED unit CDATA #IMPLIED pH CDATA #IMPLIED name CDATA #IMPLIED guiding_dye CDATA #IMPLIED > <!ELEMENT solvent (#PCDATA)> <!ATTLIST solvent name CDATA #IMPLIED > <!ELEMENT gel_conditions (first_dim?, second_dim?, solution*)> <!ATTLIST gel_conditions gel_conditions_id CDATA #IMPLIED created_date CDATA #IMPLIED modified_date CDATA #IMPLIED > <!ELEMENT first_dim (gel_info?, protein_solution?, rehydrate?, running?, load_direction?, equipment_info?)> <!ELEMENT gel_info (gel_name, ((gel_pH) | (gel_conc?, gel_bis_conc?, gel_gradient_range?))?, gel_size)> <!ELEMENT gel_name (#PCDATA)> <!ATTLIST gel_name made_by CDATA #IMPLIED > <!ELEMENT gel_pH (#PCDATA)> <!ATTLIST gel_pH low CDATA #IMPLIED high CDATA #IMPLIED > <!ELEMENT protein_solution (comment?)> <!ATTLIST protein_solution solution_id CDATA #IMPLIED solution_volume CDATA #IMPLIED solution_unit CDATA #IMPLIED protein_amount CDATA #IMPLIED protein_unit CDATA #IMPLIED guiding_dye CDATA #IMPLIED > <!ELEMENT rehydrate (#PCDATA)> <!ATTLIST rehydrate temperature CDATA #IMPLIED temperature_unit CDATA #IMPLIED time CDATA #IMPLIED time_unit CDATA #IMPLIED > <!ELEMENT running (apply+)> <!ELEMENT apply (#PCDATA)> <!ATTLIST apply step CDATA #IMPLIED current CDATA #IMPLIED current_unit CDATA #IMPLIED voltage CDATA #IMPLIED voltage_unit CDATA #IMPLIED temperature CDATA #IMPLIED temperature_unit CDATA #IMPLIED time CDATA #IMPLIED time_unit CDATA #IMPLIED power CDATA #IMPLIED power_unit CDATA #IMPLIED > <!ELEMENT load_direction (#PCDATA)> <!ELEMENT equipment_info (equipment_name)> <!ELEMENT equipment_name (#PCDATA)> <!ATTLIST equipment_name manufacturer CDATA #IMPLIED > <!ELEMENT second_dim (gel_info?, equilibrate*, running?, equipment_info?)> <!ELEMENT gel_conc (#PCDATA)> <!ATTLIST gel_conc conc CDATA #IMPLIED unit CDATA #IMPLIED > <!ELEMENT gel_bis_conc (#PCDATA)> <!ATTLIST gel_bis_conc conc CDATA #IMPLIED unit CDATA #IMPLIED > <!ELEMENT gel_gradient_range (#PCDATA)> <!ATTLIST gel_gradient_range from CDATA #IMPLIED to CDATA #IMPLIED unit CDATA #IMPLIED > <!ELEMENT gel_size (#PCDATA)> <!ATTLIST gel_size length CDATA #IMPLIED width CDATA #IMPLIED height CDATA #IMPLIED thickness CDATA #IMPLIED unit CDATA #IMPLIED > <!ELEMENT equilibrate (#PCDATA)> <!ATTLIST equilibrate step CDATA #IMPLIED solution_id CDATA #IMPLIED solution_volume CDATA #IMPLIED solution_unit CDATA #IMPLIED time CDATA #IMPLIED time_unit CDATA #IMPLIED temperature CDATA #IMPLIED temperature_unit CDATA #IMPLIED > <!ELEMENT marker_protein (marker_info+)> <!ATTLIST marker_protein marker_protein_id CDATA #IMPLIED > <!ELEMENT marker_info (item_marker+)> <!ATTLIST marker_info made_by CDATA #IMPLIED product_name CDATA #IMPLIED > <!ELEMENT item_marker (#PCDATA)> <!ATTLIST item_marker amount CDATA #IMPLIED unit CDATA #IMPLIED pi CDATA #IMPLIED pi_unit CDATA #IMPLIED MW CDATA #IMPLIED MW_unit CDATA #IMPLIED > <!ELEMENT detection (detection_method*, equipment_info?, comment?)> <!ATTLIST detection detection_id CDATA #IMPLIED > <!ELEMENT detection_method (#PCDATA)> <!ELEMENT gel_image_info (gel_author?, registration_date?, scanner?, image?, image_data?)> <!ELEMENT gel_author (person+)> <!ELEMENT registration_date (#PCDATA)> <!ELEMENT scanner (#PCDATA)> <!ATTLIST scanner manufacturer CDATA #IMPLIED > <!ELEMENT image (#PCDATA)> <!ATTLIST image url CDATA #IMPLIED width CDATA #IMPLIED height CDATA #IMPLIED unit CDATA #IMPLIED dpi CDATA #IMPLIED > <!ELEMENT image_data (#PCDATA)> <!ATTLIST image_data type CDATA #IMPLIED name CDATA #IMPLIED encoding CDATA #IMPLIED > <!ELEMENT spot_recognition (recognition_tool, property*)> <!ATTLIST spot_recognition spot_recognition_id CDATA #IMPLIED > <!ELEMENT recognition_tool (#PCDATA)> <!ATTLIST recognition_tool made_by CDATA #IMPLIED > <!ELEMENT property (#PCDATA)> <!ATTLIST property value CDATA #IMPLIED > <!ELEMENT spot_list (spot*)> <!ELEMENT spot (spot_label?, spot_location?, identification?, spot_data?, comment?)> <!ATTLIST spot accession CDATA #IMPLIED > <!ELEMENT spot_label (#PCDATA)> <!ELEMENT spot_location (spot_position, spot_volume?, spot_area?, observed_pi?, observed_MW?)> <!ELEMENT spot_position EMPTY> <!ATTLIST spot_position x CDATA #IMPLIED y CDATA #IMPLIED > <!ELEMENT spot_volume (#PCDATA)> <!ELEMENT spot_area (#PCDATA)> <!ATTLIST spot_area intensity CDATA #IMPLIED width CDATA #IMPLIED height CDATA #IMPLIED type CDATA #IMPLIED > <!ELEMENT observed_pi (#PCDATA)> <!ATTLIST observed_pi unit CDATA #IMPLIED > <!ELEMENT observed_MW (#PCDATA)> <!ATTLIST observed_MW unit CDATA #IMPLIED > <!ELEMENT identification (identification_method?, sequencing?, ms?, search_statistics*, candidate_list?, comment?)> <!ELEMENT identification_method (#PCDATA)> <!ELEMENT sequencing (sequence_exp?, equipment_info?, comment?)> <!ELEMENT sequence_exp (#PCDATA)> <!ATTLIST sequence_exp from CDATA #IMPLIED to CDATA #IMPLIED count CDATA #IMPLIED > <!ELEMENT ms (ms_peak_list?, equipment_info?, comment?)> <!ELEMENT ms_peak_list (ms_peak+)> <!ELEMENT ms_peak (#PCDATA)> <!ATTLIST ms_peak m_z CDATA #IMPLIED strength CDATA #IMPLIED > <!ELEMENT search_statistics (search_statistics_value+)> <!ATTLIST search_statistics tool_name CDATA #IMPLIED > <!ELEMENT search_statistics_value (#PCDATA)> <!ATTLIST search_statistics_value item_name CDATA #IMPLIED unit CDATA #IMPLIED > <!ELEMENT candidate_list (candidate_protein_data+)> <!ELEMENT candidate_protein_data (candidate_protein_name?, candidate_search_statistics*)> <!ATTLIST candidate_protein_data db_name CDATA #IMPLIED accession CDATA #IMPLIED > <!ELEMENT candidate_protein_name (#PCDATA)> <!ELEMENT candidate_search_statistics (search_statistics_value+)> <!ATTLIST candidate_search_statistics tool_name CDATA #IMPLIED > <!ELEMENT spot_data (protein_data?, BAD_data?, structure_data?, gene_data?, reference_list?, db_accession_list?)> <!ELEMENT protein_data (protein_name, synonym_list?, theoretical_pi?, theoretical_MW?, classification?, ec_number?, gene_ontology?, organism_from_db?, common_name_from_db?, protein_sequence?, composition_calc?, superfamily_list?, modification?, splicing?, protein_feature*)> <!ATTLIST protein_data db_name CDATA #IMPLIED accession CDATA #IMPLIED created_date CDATA #IMPLIED modified_date CDATA #IMPLIED > <!ELEMENT protein_name (#PCDATA)> <!ELEMENT synonym_list (synonym_name*)> <!ELEMENT synonym_name (#PCDATA)> <!ELEMENT theoretical_pi (#PCDATA)> <!ATTLIST theoretical_pi unit CDATA #IMPLIED > <!ELEMENT theoretical_MW (#PCDATA)> <!ATTLIST theoretical_MW unit CDATA #IMPLIED > <!ELEMENT classification (#PCDATA)> <!ELEMENT ec_number (#PCDATA)> <!ELEMENT gene_ontology (molecular_function | biological_process | cellular_component)*> <!ELEMENT molecular_function EMPTY> <!ATTLIST molecular_function go_accession CDATA #IMPLIED evidence_criteria CDATA #IMPLIED > <!ELEMENT biological_process EMPTY> <!ATTLIST biological_process go_accession CDATA #IMPLIED evidence_criteria CDATA #IMPLIED > <!ELEMENT cellular_component EMPTY> <!ATTLIST cellular_component go_accession CDATA #IMPLIED evidence_criteria CDATA #IMPLIED > <!ELEMENT organism_from_db (#PCDATA)> <!ELEMENT common_name_from_db (#PCDATA)> <!ELEMENT protein_sequence (#PCDATA)> <!ATTLIST protein_sequence start CDATA #IMPLIED end CDATA #IMPLIED count CDATA #IMPLIED type CDATA #IMPLIED > <!ELEMENT composition_calc EMPTY> <!ATTLIST composition_calc A CDATA #IMPLIED R CDATA #IMPLIED N CDATA #IMPLIED D CDATA #IMPLIED C CDATA #IMPLIED Q CDATA #IMPLIED E CDATA #IMPLIED G CDATA #IMPLIED H CDATA #IMPLIED I CDATA #IMPLIED L CDATA #IMPLIED K CDATA #IMPLIED M CDATA #IMPLIED F CDATA #IMPLIED P CDATA #IMPLIED S CDATA #IMPLIED T CDATA #IMPLIED W CDATA #IMPLIED Y CDATA #IMPLIED V CDATA #IMPLIED B CDATA #IMPLIED Z CDATA #IMPLIED X CDATA #IMPLIED > <!ELEMENT superfamily_list (superfamily+)> <!ELEMENT superfamily (#PCDATA)> <!ELEMENT modification (target_residue*)> <!ELEMENT splicing (target_residue*)> <!ELEMENT target_residue (#PCDATA)> <!ATTLIST target_residue location CDATA #IMPLIED type CDATA #IMPLIED codon CDATA #IMPLIED > <!ELEMENT protein_feature (protein_feature_type?, description?, seq_spec?, status?)> <!ATTLIST protein_feature label CDATA #IMPLIED > <!ELEMENT protein_feature_type (#PCDATA)> <!ELEMENT seq_spec (#PCDATA)> <!ELEMENT status (#PCDATA)> <!ELEMENT description (#PCDATA)> <!ELEMENT BAD_data (#PCDATA)> <!ATTLIST BAD_data accession CDATA #IMPLIED type CDATA #IMPLIED > <!ELEMENT structure_data (analysis_method?, structure_file?, domain_info?)> <!ATTLIST structure_data db_name CDATA #IMPLIED accession CDATA #IMPLIED created_date CDATA #IMPLIED modified_date CDATA #IMPLIED > <!ELEMENT analysis_method (#PCDATA)> <!ELEMENT structure_file EMPTY> <!ATTLIST structure_file url CDATA #IMPLIED format CDATA #IMPLIED > <!ELEMENT domain_info (domain+)> <!ELEMENT domain EMPTY> <!ATTLIST domain start CDATA #IMPLIED end CDATA #IMPLIED label CDATA #IMPLIED > <!ELEMENT gene_data (gene_name, locus?, gene_feature?, base_count?, nucleotide_sequence?, gene_mapping?, comment?)> <!ATTLIST gene_data db_name CDATA #IMPLIED accession CDATA #IMPLIED created_date CDATA #IMPLIED modified_date CDATA #IMPLIED > <!ELEMENT gene_name (#PCDATA)> <!ELEMENT locus (#PCDATA)> <!ELEMENT gene_feature (gene_feature_source?, cds?)> <!ELEMENT gene_feature_source (location?, qualifiers*)> <!ELEMENT location (#PCDATA)> <!ELEMENT qualifiers (#PCDATA)> <!ATTLIST qualifiers name CDATA #IMPLIED > <!ELEMENT cds (location?, qualifiers*)> <!ELEMENT base_count (#PCDATA)> <!ATTLIST base_count A CDATA #IMPLIED C CDATA #IMPLIED G CDATA #IMPLIED T CDATA #IMPLIED > <!ELEMENT nucleotide_sequence (#PCDATA)> <!ATTLIST nucleotide_sequence start CDATA #IMPLIED end CDATA #IMPLIED count CDATA #IMPLIED type CDATA #IMPLIED > <!ELEMENT gene_mapping (#PCDATA)> <!ELEMENT reference_list (reference_info*)> <!ELEMENT reference_info (reference_authors?, reference_title?, comment?)> <!ATTLIST reference_info db_name CDATA #IMPLIED accession CDATA #IMPLIED > <!ELEMENT reference_authors (#PCDATA)> <!ELEMENT reference_title (#PCDATA)> <!ELEMENT db_accession_list (db_accession_info*)> <!ELEMENT db_accession_info (mol_type?, comment?)> <!ATTLIST db_accession_info db_name CDATA #IMPLIED accession CDATA #IMPLIED > <!ELEMENT mol_type (#PCDATA)> <!ELEMENT comment (#PCDATA)> <!ELEMENT template (person*, source_info*, sample_preparation*, gel_conditions*, marker_protein*, detection*, spot_recognition*)>