% 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 % this is /tritogeneia/a/the_agora/code/trade/semiotes/bundle_syn_tex.pl bundle_syn_tex(agora_action,'Follows the syntactic rules of the particular bundle or bundles transmitted, but the overall structure must be either a list, a conjunct bundle, a disjunct bundle, or a negated bundle. Nesting of these structures is permitted.'). bundle_syn_tex(interlocutor_role,'A lower-case alphabetic string.'). bundle_syn_tex(curator_role,'A lower-case alphabetic string.'). bundle_syn_tex(agora_action_incident,'A tuple of arity 5; each argument follows its individual syntactic rules.'). bundle_syn_tex(agora_action_log,'A set of agora_action_incidents.'). bundle_syn_tex(institution,'Either an alphanumeric string, or a person''s name (automatically entered following the syntax of bundle person). For strings, both cases, dashes, underscores, commas, and ampersands are presently allowed. If you need something else, please email us.'). bundle_syn_tex(mailing_add,'A list of address-related semiotes, each following its particular syntax.'). bundle_syn_tex(rxn_sys_name,'An alphanumeric string; underscores permitted. Javascript will supply quote enclosure.'). bundle_syn_tex(coreactants_sets,'Two lists, each member obeying the rules for cpd_name. Javascript will supply functor wrapping, list delimiting, quote enclosure, and prime doubling.'). bundle_syn_tex(cpd_set,'A list, each member obeying the rules for cpd_name. Javascript will supply functor wrapping, list delimiting, quote enclosure, and prime doubling.'). bundle_syn_tex(comm_subject,'A list of comm_topics.'). bundle_syn_tex(component_rxns,'Two arguments, the first an integer and the second a bracket-delimited list of integers, each separated by a comma.'). bundle_syn_tex(nominal_pathway,'Two arguments, the first an integer and the second a bracket-delimited list of integers, each separated by a comma.'). bundle_syn_tex(nominal_pathway_name,'Two arguments, the first following the rules for rxn_name and the second a bracket-delimited list of integers, each separated by a comma.'). bundle_syn_tex(disease,'A recognized medical name for the disease and a systematic name for the species. If information on organ or tissue localization is known, given the vernacular or histological names, respectively (e.g. lung, connective tissue).'). bundle_syn_tex(markers,'The syntactic conventions for marker names differ among organisms; please use the conventions appropriate to the organism you are describing. If you have difficulty, please email us.

Within that constraint, the markers are a list of comma-separated alphanumeric strings, each with dashes, plus signs, carets, underscores, backslashes, and braces permitted. The latter four are for forming TeX-compliant Greeks, superscripts, and subscripts: see for guidance on how to enter these special characters. We''re not checking these for sense, so please be careful and ask for help if you need it.'). bundle_syn_tex(agora,'Just follow the directions!'). bundle_syn_tex(upper_bound,'Two arguments. The first is an operator from the set {<,=<,@<,@=<} (numerical less than, numerical less than or equal to, string less than, string less than or equal to, respectively). The second is either a number or any semiote or bundle.'). bundle_syn_tex(lower_bound,'Two arguments. The first is an operator from the set {>,>=,@>,@>=} (numerical greater than, numerical greater than or equal to, string greater than, string greater than or equal to, respectively). The second is either a number or any semiote or bundle.'). bundle_syn_tex(upper_bd,'A number or any semiote or bundle.'). bundle_syn_tex(lower_bd,'A number or any semiote or bundle.'). bundle_syn_tex(exclusions,'A list of semiotes or bundles, each of which must obey its own syntactic rules. Javascript will supply list delimitation, term wrapping, quote inclusion, and prime doubling.'). bundle_syn_tex(inclusions,'A list of semiotes or bundles, each of which must obey its own syntactic rules. Javascript will supply list delimitation, term wrapping, quote inclusion, and prime doubling.'). bundle_syn_tex(path_terminusa,'An alphanumeric string, spaces, underscores, dashes, and commas allowed. Javascript will supply term wrapping, quote inclusion, and prime doubling.'). bundle_syn_tex(path_terminusb,'An alphanumeric string, spaces, underscores, dashes, and commas allowed. Javascript will supply term wrapping, quote inclusion, and prime doubling.'). bundle_syn_tex(path_terminus,'An alphanumeric string, spaces, underscores, dashes, and commas allowed. Javascript will supply term wrapping, quote inclusion, and prime doubling.'). bundle_syn_tex(ec_num_id,'Four integers separated by periods, no spaces or other characters allowed.'). bundle_syn_tex(ec_num_set,'A list of ec_num_ids Javascript will supply list delimitation, term wrapping, quote inclusion, and prime doubling.'). bundle_syn_tex(organism,'Two alphabetic strings. Javascript will supply list delimitation, term wrapping, quote inclusion, and prime doubling.'). bundle_syn_tex(synonym_list,'A tuple whose functor is synonym_list, whose first argument is a legalc cpd_name or ec_num, and whose second argument is a list of legal cpd_names or ec_nums.').