% this is /tritogeneia/a/the_agora/code/trade/semiotes/semiote_semantics.pl % Release Notice % This file, and all files referenced herein that are not contributed by % someone else, are unequivocably placed in the public domain. Be mindful % that we use code, libraries, and information contributed by others, and % that they may not have released their work into the public domain. Our % goal is to release our own work, not inadvertantly place someone else's % in the public domain. % If you use, modify, redistribute, or publish anything in this file or based % on this work, we ask that you follow good scholarly practice and: % 1. cite the software system and file, or database and accession number, % as relevant, in all files or data you redistribute; % 2. reference the most current URL and archival publication for this work, % which will always be found at % http://www.biocheminfo.org/repository/current_references.html, % in your package, database, redistribution, or publication; % 3. record all your modifications to this file in a new file that % preserves this message and authorship information, contains your % authorship information and code or data, and is named with a name % different from this file's name. % The suitability of this work for any purpose is neither expressed nor implied. Use % it at your own risk! % Why we release knowledge this way is explained at % http://www.biocheminfo.org/release_notes.html % Toni Kazic, February 28, 2002 % Since the semiotes must be axiomatic, it follows that the definition of a % semiote must not call any other semiote (or bundle, for that matter). % Thus if useful things from Prolog are indispensable, they must have a % declarative definition in the semiote language (which can as well be % identical to their Prolog definition). % Each semiote takes one or more arguments. If an argument begins with a % lower-case letter, or is enclosed in single right quotes (e.g. 'X'), that % argument is understood to be a variable instantiated to the value given. % If an argument begins with an underscore (_) or capital letter then it % is an uninstantiated variable. The name of the variable is intended to % indicate the semiote's semantics (hence the very long variable names). % Multiple clauses of the same predicate, each taking a different instantiated % argument, should be read as alternative values. These are preceded by a % commented-out clause giving the variables (with long suggestive names) % for each argument. % If a semiote takes a variable then this means that the value of the variable % is not known in advance, and is supplied by a human (e.g. free text as opposed % to a menu or list of pre-defined choices). Thus we rely on the perspicacity % of the human to make sure that what is entered in the free text really corresponds % to the semiote's semantics. This is the fundamental problem of natural language % understanding --- which semiotes cannot and do not attempt to solve. % Kazic, 28.4.99. --- 14.2.00. % Note the requirement that each abbreviation have a 1:1 mapping to a % full term! abbrv(_Abbreviation). % data_action(_ActionThatCanBeTakenOnDataInADatabaseOrComputationServer). data_action(deposit). data_action(revise). data_action(review). data_action(query). data_action(curate). action_number(_SerialNumOfAnActionOnAParticularDBOrComputationServer). % db_cptn_action(_ActionThatCanBeTakenWithADatabaseOrComputationServer). db_cptn_action(enter). db_cptn_action(trade). db_cptn_action(inquire). db_cptn_action(depart). db_cptn_action(communicate). % should this be used for data and computations entering the Agora? No, % not until they've been released --- and assigned to the contributing db or % computation server with its accession. % however, need it for data entering from the other databases, % and data spooled back out to them. accession(_EntryAccessionNameOrCodeFromContributingDatabase). % However, can use this for entries within the Agora, whatever their state. % accession_status(_StatusOfAnAccessionInADatabaseOrServer). accession_status(new). accession_status(unvetted). accession_status(revised). accession_status(in_review). accession_status(reviewed). accession_status(released). accession_status(not_released). accession_status(deleted). accession_status(transferred). % entity_role(_RoleOfPersonOrEntityInDatabaseOrComputationServerProvidingOrganization). entity_role(depositor). entity_role(curator). entity_role(reviewer). entity_role(inquirer). entity_role(overseer). entity_role(contact). entity_role(communicator). entity_role(typist). % highly unusual to put a list in a semiote, but can't think of a % better way to ground this idea. Treat as a semiote for now, % Kazic, 17.6.01. % expertise(ListKeywords). expertise(_ListKeywords). % privacy_status(_PrivacyStatusOfDataOrComputation). privacy_status(publicis). privacy_status(privatus). privacy_status(nascentus). entry_id(_AgoraSerialNumber). datum_id(_AgoraSerialNumber,_Datum). prov_datum_id(_ProvisionalIDNumOfDatum,_Datum). thread_id(_ConversationSerialNumber). given_names(_GivenNames). surname(_Surname). generatnl_part(_GenrtnlPart). % Shouldn't the above one be, Geetha 9-05-03 % generatnl_part(Jr.). % generatnl_part(Sr.). % generatnl_part(I). % generatnl_part(II). % generatnl_part(III). % generatnl_part(IV). % generatnl_part(V). % generatnl_part(VI). % generatnl_part(VII). % generatnl_part(VIII). entity_name(_NameOfForProfitOrNonProfitEntity). department(_OrganizationalComponentOfInstitution). room(_RoomNumber). building(_BuildingNameOrNumber). street_name(_StreetOrRoadNameOrNumber). street_number(_AlphaNumericStreetAddress). district(_DistrictNameOrDesignation). institutional_mail_code(_InstMailCode). national_mail_code(_NatlMailCode). city(_VillageOrTownOrCity). geo_state(_StateOrProvinceOrCounty). nation(_Nation). telephone_country_code(_TelephoneCountryCode). telephone_city_code(_TelephoneCityOrAreaCode). telephone_local_number(_TelephoneNumberAsDialedFromOutsideTheCity). email_add(_InternetEmailAddress). comm_msg(_TextOfMessageBody). topic(_TopicOfCommunication). comm_attchmt(_EmailAttachment). comm_sender(email_add(_InternetEmailAddress)). comm_recipient(email_add(_InternetEmailAddress)). mime_type(_FileMimeType). url(_URLOfIncludedFileOrWebSite). alista(_ListOfAnything). alistb(_ListOfAnything). % need to call system to get this datum from AgoraServer. % It probably makes most sense to do it % from prolog, rather than at the intermediate stages in the process. This % can now be done using utc:utc_timestamp and related predicates. utc_time(_UTCUnix32bitTimeStampOnAgoraServer). local_time(_LocalTimeAtom,_HostNameLocalMachine). synonym(_PrimaryTermInTheAgora,_SecondaryTerm). cpd_name(_NameOfAMoleculeOrMolecularComplex). stoich(_StoichiometryOfSpeciesInReaction). mol_state(_StateOfAMolecularSpeciesInAParticularReaction). macromol(_BinaryIsOrIsnt). num_subunits(_NumCovalentlyBondedSubunitsInMol). compartment(_CompartmentOfAMolecularSpeciesInAParticularReaction). dalton(_MolWt). % Adding compartment_rev, Geetha 9-05-03 compartment_rev(_ReviewOfCompartment). rxn_role(catalyst). rxn_role(noncatalyst). rxn_role(either). rxn_name(_NameForAReactionOrSetOfReactions). rxn_type_name(_NameForABiochemicalTypeOfReaction). path_process_name(_NameForASetOfReactionsSoDesignatedHistorically). % Adding type_person, but this is the same as entity_role. Why do we need both, Geetha 9-05-03 type_person(depositor). type_person(communicator). type_person(reviewer). type_person(typist). type_person(revisor). type_person(user). type_person(overseer). type_person(contact). % Adding classtn_qual, Geetha 9-05-03 classtn_qual(suggested). classtn_qual(official). classtn_qual(unknown). ec_class(_Class). ec_subclass(_SubClass). ec_subsubclass(_SubSubClass). ec_serial_num(_SerialNum). isosmiles(_IsomericSmilesString). genus(_Genus). species(_Species). strain(_Strain). approx_org_name(_ApproxNameOfOrganism). marker(_Marker). genetic_background(_Background). encoding_loci(_ListOfLociEncodingAProduct). tissue(_Tissue). organ(_Organ). cell_type(_CellType). cell_line(_CellLine). rlted_db(_NameOfDataSource). % Shouldn't the above one be, Geetha 9-05-03 % rlted_db(umbbd). % rlted_db(nc). % rlted_db(klotho). % rlted_db(atropos). % rlted_db(lachesis). % rlted_db(moirai). % rlted_db(brenda). % rlted_db(nist). % rlted_db(enzyme). % rlted_db(expasy). % rlted_db(ddbj). % rlted_db(genbank). % rlted_db(ligand). % rlted_db(chemfinder). % rlted_db(kegg). % rlted_db(wdcm). % rlted_db(atcc). % rlted_db(taxos). % rlted_db(swissport). % rlted_db(pir). % rlted_db(emb). % rlted_db(tremb). % rlted_db(pdb). % rlted_db(ndb). % rlted_db(Medline). % rlted_db(PubMed). % rlted_db(Chemical Abstracts Service). % rlted_db(None). % rlted_db(Unknown). rlted_url(_URL). search_string(_SearchString). search_url(_URLOfSeachEngine). file_type(_FileType). % Shouldn't the above one be, Geetha 9-05-03 % file_type(eps). % file_type(gif). % file_type(pdb). % file_type(ps). % file_type(tex). % file_type(ltx). % file_type(txt). % file_type(ascii). % file_type(mmcif). % file_type(jpeg). % file_type(molfile). % file_type(isosmile). % file_type(smile). % file_type(html). % file_type(js). % file_type(perl). % file_type(prolog). % file_type(c). % file_type(out). % file_type(qof). % file_type(java). % file_type(phtshp). % file_type(gz). % file_type(gzip). % file_type(tar). % file_type(Z). % file_type(dialog). % file_type(config). % file_type(term). % file_type(fischer). file(_FullPathFileNameOrAbsoluteURL). compression_algorithm(_CompressionAlgorithm). compression_status(_CompressionStatus). compression_os(_CompressionClassOfOperatingSystem). % Shouldn't the above 2 be, Geetha 9-05-03 % compression_status(0). % compression_status(1). % compression_os(unix). % compression_os(pc). %compression_os(mac). %compression_os(linux). encoding_status(_EncodingStatus). encoding_algorithm(_EncodingAlgorithm). encoding_os(_EncodingClassOfOperatingSystem). agora_citation_key(_AgoraCitationKey). temp_agora_citkey(_TempRefSerialNumberSuppliedByMySql). % what about medline_uid? these are all overlapping! alt_cit_id(_AltCitIdNumOrString). % citation_type(_TypeOfPublication). citation_type(article). citation_type(book). citation_type(inbook). citation_type(inproceedings). citation_type(techreport). citation_type(unpublished). citation_type(pc). citation_type(phdthesis). citation_type(msthesis). citation_type(url). article_title(_TitleString). journal_title(_TitleString). volume(_VolumeNumber). start_page(_StartingPageNumber). end_page(_EndingPageNumber). year(_YearInXXXXFormat). abstract(_AbstractTextString). book_title(_TitleString). series_title(_TitleString). edition(_EditionOrdinalNumber). isbn(_ISBNSerialNumber). method(_StringOrAgoraCitationKeyDescribingMethod). % do we need a semiote to flag a bundle? think so bundle(_Bundle). num_steps(_NumberOfStepsInPath). functor_name(_Functor). list_num(_NumberOfAList). inclusive_op(Operator) :- ( Operator == '>=' ; Operator == '=<' ; Operator == '@>=' ; Operator == '@=<' ). exclusive_op(Operator) :- ( Operator == '>' ; Operator == '<' ; Operator == '@>' ; Operator == '@<' ). bound(Bound) :- ( number(Bound) ; compound(Bound) ). chosen_action(_FormAction). % Shouldn't the above one be % chosen_action(more). % chosen_action(next). % Geetha, 9-5-03 % new 2.6.00. user_name(_BriefUniqueStringIndentifyingAgoraUser). user_password(_EncryptedPasswordForUserName). secret_question(_EncryptedStringOfOneQuestion). secret_answer(_EncryptedStringOfAnswerToSecretQuestion). output_format(_UserSpecifiedOutputFormat). % Add. % Jiang 14.04.2003 % Adding the arguments needed in the parenthesis for all these semiotes, % Geetha 9-2-03 Need to check with Toni. multistep_q(_MultipleSteps). mech_info_q(_MechanicalInformation). disease_q(_Disease). phys_char_q(_PhysicalCharacterestics). other_orgs_q(_OtherOrganisms). alt_rxns_q(_AlternateReactions). alt_cat_rxns_q(_AlternateCatalystReactions). alt_forms_mol_q(_AlternateFormsMolecule). mol_specificity_q(_MolecularSpecificity). voltage_act_q(_VoltageActivated). % Since it is a bundle of sa_class, sa_subclass etc, saier_num is not needed here. % Geetha 9-04-03 % saier_num(_). sa_class(_Class). sa_subclass(_SubClass). sa_family(_SaierFamily). sa_subfamily(_SaierSubFamily). sa_protein(_SaierProtien). rxn_survey(_ReactionSurvery). org_survey(_OrganismSurvey). reference_number(_ReferenceNumber). stimulus_sen(_Stimulus). % Check with Toni, Is this the right way to do it %stimulus_src(_). stimulus_src(intracellular). stimulus_src(enviornmental). stimulus_src(either). %stimulus_resp(_). stimulus_resp(increased). stimulus_resp(decreased). stimulus_resp(either). stimulus_name(_StimulusName). stimulus_mech_known(_KnownStimulusMechanism). rxn_ref(_ReactionReference). kin_survey(_KineticSurvey). % I don't think we need this, Geetha 9-04-03 %cata_survey2(_). %trans_survey2(_). %org_survey2(_). primary_term(_PrimaryTerm). config(_Configuration). db_value(_DatabaseValue). accession_number(_AccessionNumber). database_set(_DatabaseSet). kin_order_rev(_ReviewOfKineticOrder). type_kin_q_rev(_). kin_syl_rev(_). assay_results_rev(_ReviewOfAssayResults). strain_rev(_ReviewOfStrain). genetic_background_rev(_ReviewOfGeneticBackground). markers_rev(_ReviewOfMarkers). tissue_rev(_ReviewOfTissue). cell_type_rev(_ReviewOfCellType). cell_line_rev(_ReviewOfCellLine). rxn_catalyzed_rev(_ReviewOfCatalyzedReaction). rxn_transport_rev(_ReviewOfTransportReaction). rxn_has_macromol_rev(_ReviewofReactionThatHasMacromol). rxn_novel_macromol_rev(_ReviewofNovelMacromolReaction). syno_review_list(_ListofSynonymReview). syno_review(_ReviewOfSynonyms). catalyst_review(_ReviewOfCatalyst). trans_review(_ReviewOfTransport). kin_review(_ReviewOfKinetics). % What is the difference between rxn_review/reacation_review, organ_rev/org_review and alt_rxns_q_rev/alt_rxns_review % Geetha 9-04-03 org_review(_ReviewOfOrganisms). organ_rev(_ReviewOfOrganism). alt_rxns_q_rev(_ReviewofAlternateReactions). alt_rxns_review(_). rxn_review(_ReviewOfReaction). reaction_review(_). %catalyst_review2(_). %trans_review2(_). %org_review2(_). horiz_rxn_review(_ReviewOfHorizontalReaction). dep_comments_review(_ReviewofCommentsForDeposit). compound_isosmiles_str(_). %%%%%%%%%%%%%%%%%% deprecated semiotes % abolished --- these are not semiotes! They're only here as examples of what not to do. % sinistra_entry(_ListSinistralateralCpds). % dextra_entry(_ListDextralateralCpds). % cofactor_entry(_ListBilateralCpds). % sinistra_stoich(_ListStoichiometriesOfSinistraEntry). % dextra_stoich(_ListStoichiometriesOfDextraEntry). % cofactor_stoich(_ListStoichiometriesOfCofactorEntry).