<!-- 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*)>