% 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. 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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 % this is /tritogeneia/a/the_agora/code/trade/semiotes/bundle_sem_tex.pl bundle_sem_tex(agora_action,'The bundle of semiotes transmitted to or from the Agora for a given interaction in the Agora. The bundle must include either the bundle dcb or \sp{ccb}. These should be silently added by the interface without user input.'). bundle_sem_tex(interlocutor_role,'The role a human or program --- the interlocutor --- performs in the Agora when interacting with the offered data and programs in a particular transaction. These are: depositor -- an interlocutor who deposits new data; reviser -- an interlocutor who revises existing data already offered in the Agora; reviewer -- an external interlocutor who critically peer-reviews deposited data before its public release; user -- an interlocutor who uses public data.'). bundle_sem_tex(curator_role,'The role an entity, human or computational, plays in developing, maintaining, or otherwise curating a database or computation offered in the Agora. These roles are: overseer --- the person of final authority and responsibility; contact --- the person whom interlocutors should contact; communicator --- an entity which accepts, rejects, or modifies information in a non-public or informal way; and typist --- the data entry person or program. Communicator and typist can easily vary by datum or computation; contact may, depending on the organization of the database or server; but overseer should be constant for a given database or server, though it may vary over time. An entity may include one or more subentities --- two people, a person and a program, etc.'). bundle_sem_tex(institution,'A nonprofit or for-profit organization. If you are a private individual acting independently of any organization, please check the box labelled `use my name''.'). bundle_sem_tex(entity,'An entity is either a person, an organization, or a software system (either databases or computation server or algorithms).'). bundle_sem_tex(data_authority,'The entity which regards the given datum as correct.'). bundle_sem_tex(cptn_authority,'The entity which regards the given computation as correct.'). bundle_sem_tex(agora_action_incident,'An entry into the agora_action_log denoting each transaction in the Agora and its serial number, person initiating the action, the type of action, the central timestamp of the action, and the action itself.'). bundle_sem_tex(rxn_sys_name,'The official, systematic name for a reaction as determined by the Nomenclature Committee of the IUBMB.'). bundle_sem_tex(coreactants_sets,'Two lists of molecules, each list a group of molecules which react together (are on the same side of a reaction equation).'). bundle_sem_tex(cpd_set,'Any list of molecules; there need be no relationship among the list members.'). bundle_sem_tex(component_rxns,'For a reaction, path, pathway, or process identified by its datum_id, a list of datum_ids for reactions, paths, pathways, processes, or any combination thereof, which when combined produce the formal reaction equation of the first reaction (path, pathway, or process).'). bundle_sem_tex(nominal_pathway_abbrv,'Two arguments, the first the primary term used as the name of the pathway, as historically defined, in The Agora; and the second an abbreviation for the pathway.'). bundle_sem_tex(nominal_pathway,'Two arguments, the first the datum_id of reaction whose formal reaction equation equals the combination of reaction equations of its component reactions, and which has historically been called a `pathway'' in the biochemical or molecular biological literature; and the second the datum_ids of the corresponding component_rxns.'). bundle_sem_tex(nominal_pathway_name,'Two arguments, the first the Agora''s primary name for a reaction whose formal reaction equation equals the combination of reaction equations of its component reactions, and which has historically been called a `pathway'' in the biochemical or molecular biological literature; and the second the datum_ids of the corresponding component_rxns.'). bundle_sem_tex(agora_action_log,'The set of all agora_action_incidents.'). bundle_sem_tex(mailing_add,'Your address for postal and courier services (no post office boxes!). The address must include the numerical address and name of the street, road, or highway for the building; the name of the city, town, or village; the name of the nation; and any national postal codes used by your country. If the following are used, they can be specified: the number of your room (this mandates including the number or name of your building); the name of your building; your institution''s name; a mail code, stop, or box used within your institution (this will trigger inclusion of your institution''s name automatically); the district within your city; and the state or province of the city.'). bundle_sem_tex(vox_telephone,'Your telephone number used for voice conversations.'). bundle_sem_tex(fax_telephone,'Your telephone number used for fax transmission and reception.'). bundle_sem_tex(human_location,'Your complete location, including department, institution, mailing address, email address, and telephone numbers. This is computed from the information you have already provided.'). bundle_sem_tex(entity_location,'Your complete location, including department, institution, mailing address, email address, and telephone numbers, assuming you are not human. This is computed from the information you have already provided.'). bundle_sem_tex(comm_subject,'The topic of an email message or comment.'). bundle_sem_tex(comm_inclusion,'The URL and MIME type of a file included indirectly (not as plain ASCII) in an email message or other communication.'). bundle_sem_tex(entry,'An entry, either of a database datum, a set of such data, or an archived computation. What constitutes an entry is likely to evolve and so the semantics of this bundle is not yet fixed --- 30.4.99.'). bundle_sem_tex(datum_origin,'The origin of a datum or computational result: allowed values are extensional and intensional.'). bundle_sem_tex(db_synonym,'A tuple of synonyms from a contributing database, consisting first of the primary term in that database; second a synonym for that term from that database; and finally an abbreviation for the contributing database.'). bundle_sem_tex(synonym_list,'A tuple, consisting first of the Agora''s primary term for that term; and second, a comma-delimited list of synonyms, each synonym either a cpd_name or an ec_num. The primary term can be either a compound''s name or an ec_num.'). bundle_sem_tex(compound_id,'The serial number of a compound.'). bundle_sem_tex(config,'A Klotho configuration rule for specifying the stereochemical structure of the named compound.'). bundle_sem_tex(prov_rxn_eqn,'A reaction equation as entered into the Agora''s databases. It is provisional in that it is subject to further error-checking; it will not be assigned a serial number until this is completed.'). bundle_sem_tex(state_list,'The list of states. Allowed values are `free'' and `bound''; if you need other states please email us.'). bundle_sem_tex(rxn_desc,'A text string describing a reaction. This is only for processing legacy data, and will not be permitted as a way of entering information about reactions, however ill defined they may be.'). bundle_sem_tex(datum_status,'For any extensional datum, whether that datum is proposed, officially assigned, deleted, or transferred.'). bundle_sem_tex(organism,'The formal binomial name for an organism, as shown in the reference taxonomic database.'). bundle_sem_tex(disease_related,'A tuple consisting of two arguments. The first is the bundle disease; the second is either of the bundles ec_num or \sp{compound}.'). bundle_sem_tex(disease,'A clinical disease or syndrome, of any species. If the disease is localized to a particular tissue or organ, please enter that information in the appropriate box(es).'). bundle_sem_tex(organism_strain,'A named genetic variant or serotype of an organism.'). bundle_sem_tex(encoding_loci,'The gene or genes encoding the named macromolecule.'). bundle_sem_tex(markers,'The gene or genes whose alleles are different from those in the genetic background of this strain of the organism.'). bundle_sem_tex(compound_name,'The primary term used to reference a molecule, molecular complex, ion, or molecular assembly, for all molecules or pseudo-molecules (such as genes) of interest, independent of their structure. The name itself may be a trivial, biochemical, or IUPAC name; but it must be the primary name used for that molecular entity in the Agora. A compound may have many synonymous names, but only one compound_name.'). bundle_sem_tex(compound_isosmiles,'A tuple whose first argument is the value of a compound_name and whose second argument is an isomeric SMILES string.'). bundle_sem_tex(journal_abbrv,'An abbreviation and full title of a journal.'). bundle_sem_tex(publisher_abbrv,'An abbreviation and full title of a publisher.'). bundle_sem_tex(address_abbrv,'An abbreviation and full title of a publisher''s address.'). % here the url is the one for the public site! bundle_sem_tex(agora,'The Agora is a medium for sharing curatorial functions among independent databases. END, BND, UM-BBD, and Moirai now participate. A key component is the language Glossa ( a 283 KB PostScript file or ( a 298 KB PDF file).

The name is derived from an essential feature of cities, towns, and villages in ancient Greece and the Greek-speaking world. The agora was a combination public square, marketplace, law court, restaurant district, government seat, and mall. It was the place everyone went to hang out and exchange ideas, goods, and services, from philosophy to chickens to a variety of recreations; to promenade, argue, linger, and enjoy. Teenagers cruised the agora just as they do now in malls, public parks, and town centers throughout the world. Then as now, this cruising produced consternation in their elders, who sometimes passed laws forbidding such activity. Many "transactions" were not financial, but the larger notion of exchange was fundamental to all of them.

Similarly, we hope the Agora will become a virtual meeting place for exchanging ideas, data, and computations about biology.'). bundle_sem_tex(upper_bound,'A datum to be used as an upper bound in extracting a range of values, together with the operator specifying whether the datum is included or excluded from the range of values.'). bundle_sem_tex(upper_bd,'A datum to be used as an upper bound in extracting a range of values. The operation is assumed to be inclusive.'). bundle_sem_tex(lower_bound,'A datum to be used as a lower bound in extracting a range of values, together with the operator specifying whether the datum is included or excluded from the range of values.'). bundle_sem_tex(lower_bd,'A datum to be used as a lower bound in extracting a range of values. The operation is assumed to be inclusive.'). bundle_sem_tex(exclusions,'A list of bundles or semiotes whose values, either jointly or individually, are not present in, or used to compute, the answer to a query.'). bundle_sem_tex(inclusions,'A list of bundles or semiotes whose values, either jointly or individually, must be present in, or used to compute, the answer to a query.'). bundle_sem_tex(path_terminusa,'In a path, a node having only one edge, and different from any other such node.'). bundle_sem_tex(path_terminusb,'In a path, a node having only one edge, and different from any other such node.'). bundle_sem_tex(path_terminus,'In a path, a node having only one edge, and different from any other such node.'). bundle_sem_tex(ec_num_id,'The EC number of a reaction, expressed as a single string.'). bundle_sem_tex(ec_num_set,'A group of ec_num_ids. '). bundle_sem_tex(ec_group,'A class, subclass, or subsubclass of the Enzyme Nomenclature.').