Regulatory elements ------------------- All following tables contain lists of correspondent regulatory elements. Common fields: _guid - unique identifier pkg_guid - determine package (link to packages) art_guid - determine article (link to articles) genome_guid - determine genome (link to dict_genomes) name - regulatory element name fl_real_name - boolean, determine whether name is "real" (i.e. does it belong to some systematic nomenclature or was introduced by article authors) descript - some description in free form effectors genes location - textual description of gene location ref_bank1 - databank reference ref_bank2 - -//- ref_bank3 - -//- ref_bank4 - -//- signature - DNA sequence (long enough to determine gene in genome) metabol_path - metabolic pathway ferment_num - EC number gene_function - short description of gene function helices - determine secondary structure sec_struct_guid - corresponding secondary structure (link to sec_structures) pos_from1 - start position of the first stem pos_to1 - end position of the first stem pos_from2 - start position of the second stem pos_to2 - end position of the second stem locuses location - textual description of gene location operons regulators fl_prot_rna - protein or RNA regulator_type_guid - type of regulator (link to dict_regulator_types) gene_guid - corresponding gene (link to gene encoding the regulator) ref_bank1 - databank reference ref_bank2 - -//- ref_bank3 - -//- ref_bank4 - -//- consensus - binding site consesus sequence family - family of regulators regulons regulator_guid - determine corresponding regulator (link to regulators) sec_structures pos_from - start position (relative to some regulatory element) pos_from_guid - regulatory element to which start of the secondary structure is binded (link to some table with regulatory elements) pfo_type_id - type of this regulatory element (link to obj_types) pfo_side_guid - location in this regulatory element to which start is binded (e.g. start, end, transcription start, translation start etc.; link to dict_obj_side_types) pos_to - end position (relative to some regulatory element) pos_to_guid - regulatory element dto which end position is binded (link to some table with regulatory elements) pto_type_id - type of this regulatory element (link to obj_types) pto_side_guid - location in this regulatory element to which end is binded (e.g. start, end, transcription start, translation start etc.; link to dict_obj_side_types) sequence - secondary structure sequence sites func_site_type_guid - functional type (link to dict_func_site_types) struct_site_type_guid - structural type (link to dict_struct_site_types) regulator_guid - corresponding regulator (link to regulators) fl_dna_rna - DNA or RNA pos_from - start position (relative to some regulatory element) pos_from_guid - regulatory element to which start of the secondary structure is binded (link to some table with regulatory elements) pfo_type_id - type of this regulatory element (link to obj_types) pfo_side_guid - location in this regulatory element to which start is binded (e.g. start, end, transcription start, translation start etc.; link to dict_obj_side_types) pos_to - end position (relative to some regulatory element) pos_to_guid - regulatory element to which end position is binded (link to some table with regulatory elements) pto_type_id - type of this regulatory element (link to obj_types) pto_side_guid - location in this regulatory element to which end is binded (e.g. start, end, transcription start, translation start etc.; link to dict_obj_side_types) site_len - site length sequence - site sequence (a number can be placed within this field to represent a particular length of unknown sequence (N's) signature - site signature (part of sequence long enough to find site in genome reliably if site sequence is too short) (a number can be placed within this field to represent a particular length of unknown sequence (N's) transcripts pos_from - start position (relative to some regulatory element) pos_from_guid - regulatory element to which start of the secondary structure is binded (link to some table with regulatory elements) pfo_type_id - type of this regulatory element (link to obj_types) pfo_side_guid - location in this regulatory element to which start is binded (e.g. start, end, transcription start, translation start etc.; link to dict_obj_side_types) pos_to - end position (relative to some regulatory element) pos_to_guid - regulatory element dto which end position is binded (link to some table with regulatory elements) pto_type_id - type of this regulatory element (link to obj_types) pto_side_guid - location in this regulatory element to which end is binded (e.g. start, end, transcription start, translation start etc.; link to dict_obj_side_types) tr_len - transcript length --------------------------------------------------------------------------------------------------------------------------------------- Data hierarchy -------------- packages pkg_guid - unique identifier title - package title annotator_id - id of annotator working with this package (link to db_users) article_num - number of articles in package pkg_state - 1 - just created, 2 - sent for annotation, 3 - annotated, 4 - returned to annotator for correction, 5 - accepted into database pkg_state_date - date of last pkg_state modification articles art_guid - unique identifier pkg_guid - determine package (link to packages) title - article title author - article author pmid - PubMed ID art_journal - journal name art_year - year of publication art_month - month of publication art_volume - volume of journal art_issue - issue of journal art_pages - pages art_abstruct - abstract exp_num - number of experiments described art_state - 0 - not yet reviewed, 1 - currently reviewed, 2 - review completed, 3 - article is unrelated, 4 - article is unclear experiments exp_guid - unique identifier pkg_guid - determine package (link to packages) art_guid - determine article (link to articles) descript - text description --------------------------------------------------------------------------------------------------------------------------------------- Experiment types ---------------- exp2result_types - matches experiment with all its result type pkg_guid - determine package (link to packages) art_guid - determine article (link to articles) exp_guid - determine experiment (link to experiments) exp_result_type_guid - determine result type exp2technique_types - matches experiment with all its technique type pkg_guid - determine package (link to packages) art_guid - determine article (link to articles) exp_guid - determine experiment (link to experiments) exp_technique_type_guid - determine technique type exp_sub_objects - matches an experiment with all its subobjects pkg_guid - determine package (link to packages) art_guid - determine article (link to articles) exp_guid - determine experiment (link to experiments) obj_guid - determine linked object obj_type_id - type of linked object order_num - number in list of all subobjects for a given experiment (to keep their order) strand - DNA strand where subobject reside (where applied) reg_elem_sub_objects - matches an regulatory element with all its subobjects pkg_guid - determine package (link to packages) art_guid - determine article (link to articles) parent_guid - determine regulatory element (link to some regulatory elements table) parent_type_id - regulatory element type (link to obj_types) child_guid - determine subobject (link to some regulatory element table) child_type_id - subobject type (link to obj_types) child_n - index of children (to keep their order) strand - DNA strand where subobject reside (where applied) --------------------------------------------------------------------------------------------------------------------------------------- Dictionaries/vocabularies ------------------------- Common fields: _guid - unique identifier name - text value dict_exp_result_types - possible experiment result types (site prediction, promoter mapping etc.) dict_exp_technique_types - possible experiment technique types (southern blot, footprinitng etc.) dict_func_site_types - possible functional site types (activator, promoter etc.) dict_genomes - genomes dict_obj_side_types - possible locations of binding to other regulatory elements (begin/end, transcription start/end etc.) dict_regulator_types - possible regulator types dict_struct_site_types - possible types of structural sites (palindrome, tandem repeat etc.) --------------------------------------------------------------------------------------------------------------------------------------- Dictionary correspondence ------------------------- These tables contatains matches between dictionaries from XML files and those, stored in database in corresponding dict_* tables. Common fields: pkg_name - value from XML db_name - value from database h_dict_exp_result_types h_dict_exp_technique_types h_dict_func_site_types h_dict_genomes h_dict_obj_side_types h_dict_regulator_types h_dict_struct_site_types --------------------------------------------------------------------------------------------------------------------------------------- System ------ db_user_roles - possible roles of users - curator and annotator id - id role_name - name db_users - lists of database users id user_role_id - curator or annotator (link to db_user_roles) name - internal identifier full_name - surname and initials phone - contact phone email - e-mail address fl_active - active/not-active guids - maximal used guid for every object type obj_type - object type (link to obj_types) max_guid - maximal value obj_name_genomes - store genomes for every regulatory element obj_guid - GUID for regulatory element pkg_guid - determine package art_guid - determine article name - genome name genome_guid - determine genome obj_type_id - determine regulatory element type obj_sub_types - define regulator types hierarchy parent_obj_type_id - parent type id (link to obj_type or 0 if child type can exists on its own) child_obj_type_id - child type id (link to obj_type) obj_synonyms - define synonym for an object pkg_guid, art_guid - determine article obj_guid - determine object syn_name - synonym fl_real_name - boolean, whether this synonym is "real" obj_types - possible regulatory elements types id - id for links obj_type_name - name of regulatory element type obj_tbname - name of corresponding database table (usually simply plural form of the type name) cp_order - index of type (to keep their order) pkg_history - history of operations with packages pkg_guid - determine package (link to packages) event_date - date of operation event_operation - description of operation user_by_id - id of user who performed operation user_by_name - name of user who performed operation user_by_role - role of user who performed operation user_by_email - email of user who performed operation user_by_phone - phone number of user who performed operation user_to_id - id of user who participate in operation user_to_name - name of user who participate in operation user_to_role - role of user who participate in operation user_to_email - e-mail of user who participate in operation user_to_phone - phone number of user who participate in operation