Continued updates to the pub module. Added a warning to the bulk loader to fail if the table description cannot be found. This could happen if a loader uses a custom table and the loader is exported to another database without the custom table

tripal_bulk_loader/tripal_bulk_loader.loader.inc

@@ -497,6 +497,12 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
 
   // get the table description
   $table_desc = tripal_core_get_chado_table_schema($table);
+  if (!$table_desc) {
+    watchdog('T_bulk_loader', "Failure: Tripal does not know about the table named %table. If this is a custom table, 
+      please define it first", array(), WATCHDOG_ERROR);
+    $data[$priority]['error'] = TRUE;
+    return;  
+  }
 
   // Check that template required fields are present. if a required field is
   // missing and this
@@ -587,12 +593,13 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
     $table_data['update_if_duplicate'] = 0;
   }
 
-  // if "select if duplicate" is enabled then check to ensure unique constraint is not violoated.
-  // If it is violoated then simply return, the record already exists in the database.
+  // if "select if duplicate" is enabled then check to ensure unique constraint is not violated.
+  // If it is violated then simply return, the record already exists in the database.
   // We check for "insert_unique" for backwards compatibilty but that mode no longer exists
   $data[$priority]['is_duplicate'] = 0;
   if (preg_match('/insert_unique/', $table_data['mode']) or
-     $table_data['select_if_duplicate'] == 1 or $table_data['update_if_duplicate'] == 1) {
+     $table_data['select_if_duplicate'] == 1 or 
+     $table_data['update_if_duplicate'] == 1) {
     $options = array('is_duplicate' => TRUE);
     $duplicate = tripal_core_chado_select($table, array_keys($table_desc['fields']), $values, $options);
 

tripal_pub/e_utilities.pl

@@ -1,61 +0,0 @@
-#!/usr/bin/perl -w
-# ---------------------------------------------------------------------------
-# Define library for the 'get' function used in the next section.
-# $utils contains route for the utilities.
-# $db, $query, and $report may be supplied by the user when prompted; 
-# if not answered, default values, will be assigned as shown below.
-
-use LWP::Simple;
-use utf8;
-
-my $utils = "http://www.ncbi.nlm.nih.gov/entrez/eutils";
-
-my $db     = "Pubmed";
-my $query  = $ARGV[0];
-my $report = $ARGV[1];
-
-# ---------------------------------------------------------------------------
-# $esearch contÁins the PATH & parameters for the ESearch call
-# $esearch_result containts the result of the ESearch call
-# the results are displayed Ánd parsed into variables 
-# $Count, $QueryKey, and $WebEnv for later use and then displayed.
-
-my $esearch = "$utils/esearch.fcgi?" .
-              "db=$db&retmax=1&usehistory=y&term=";
-
-my $esearch_result = get($esearch . $query);
-
-
-
-$esearch_result =~ 
-  m|<Count>(\d+)</Count>.*<QueryKey>(\d+)</QueryKey>.*<WebEnv>(\S+)</WebEnv>|s;
-
-my $Count    = $1;
-my $QueryKey = $2;
-my $WebEnv   = $3;
-
-# ---------------------------------------------------------------------------
-# this area defines a loop which will display $retmax citation results from 
-# Efetch each time the the Enter Key is pressed, after a prompt.
-
-my $retstart;
-my $retmax=3;
-
-for($retstart = 0; $retstart < $Count; $retstart += $retmax) {
-  my $efetch = "$utils/efetch.fcgi?" .
-               "rettype=$report&retmode=text&retstart=$retstart&retmax=$retmax&" .
-               "db=$db&query_key=$QueryKey&WebEnv=$WebEnv";
-	
-  #print "\nEF_QUERY=$efetch\n";     
-
-
-  my $efetch_result = get($efetch);
-
-	#open( $fh, '>', \$efetch_result);
-
-  
-  print $efetch_result;
-    
-  #print binmode($fh, ":utf8");
-  
-}

tripal_pub/includes/tripal_pub.admin.inc

@@ -144,6 +144,7 @@ function theme_tripal_pub_importer_setup_form($form) {
 function tripal_pub_importer_setup_form(&$form_state = NULL, $pub_import_id = NULL, $action = 'new') {
   tripal_core_ahah_init_form();
 
+  dpm($form_state);
   
   // Set the default values. If the pub_import_id isn't already defined by the form values 
   // and one is provided then look it up in the database

tripal_pub/pub_types.txt

@@ -1,932 +0,0 @@
-[Term]
-id: TPUB:0000100
-name: abbreviations
-def: Works consisting of lists of shortened forms of written words or phrases used for brevity. Acronyms are included here.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: abstracts
-def: Works consisting of lists of publications on a subject and that provide full annotated bibliographical information together with substantive summaries or condensations of the facts, ideas, or opinions presented in each publication listed. (From LC Subject Cataloging Manual)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: academic_dissertations
-def: Works consisting of formal presentations made usually to fulfill requirements for an academic degree.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: addresses
-def: Works consisting of speeches, orations, or written statements, usually formal, directed to a particular group of persons. These are different from LECTURES that are usually delivered to classes for instructional purposes.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: almanacs
-def: Works consisting of a calendar of days, weeks, and months, together with information such as astronomical data, various statistics, etc. (From Genre Terms: A Thesaurus for Use in Rare Book and Special Collections Cataloguing, 2d ed)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: anecdotes
-def: Works consisting of brief accounts or narratives of incidents or events.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: animation
-def: A film or video wholly or partially created by photographing drawings, sculptures, or other inanimate things in sequence to create the illusion of motion. Animations are also generated by computers. (From Moving Image Materials: Genre Terms, 1988)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: annual_reports
-def: Works consisting of annual statements concerning the administrative and operational functions of an institution or organization.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: atlases
-def: Works consisting of collections of illustrative plates, charts, etc., usually with explanatory captions.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: autobiography
-def: Works consisting of self-described accounts.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: bibliography
-def: A work consisting of a list of books, articles, documents, publications, and other items, usually on a single subject or related subjects.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: biobibliography
-def: Works consisting of biographical information as well as lists of the writings of those persons.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: biography
-def: Works consisting of an account of the events, works, and achievements, personal and professional, during a person's life. It includes articles on the activities and accomplishments of living persons as well as the presentation of an obituary.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: book_illustrations
-def: Works consisting of photographs, prints, drawings, portraits, plates, diagrams, facsimiles, maps, tables, or other representations or systematic arrangements of data designed to elucidate or decorate the contents of a publication. (From The ALA Glossary of Library and Information Science, 1983, p114)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: book_reviews
-def: Works consisting of critical analyses of books or other monographic works.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: bookplates
-def: Works consisting of book owner's identification labels. They are usually intended for attaching inside a book or similar object. (From Thesaurus for Graphic Materials II: Genre and Physical Characteristic Terms, 1995)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: cartoons
-def: Images used to comment on such things as contemporary events, social habits, or political trends; usually executed in a broad or abbreviated manner.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: case_reports
-def: Clinical presentations that may be followed by evaluative studies that eventually lead to a diagnosis.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: catalogs
-def: Works consisting of bibliographic records, created according to specific and uniform principles of construction and under the control of an authority file, which describe the materials contained in a collection, library, or group of libraries. Catalogs include also lists of materials prepared for a particular purpose, such as exhibition catalogs, sales catalogs, garden catalogs, medical supply catalogs. (From The ALA Glossary of Library and Information Sciences, 1983)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: charts
-def: Information presented in graphic form, for example, graphs or diagrams.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: chronology
-def: Works consisting of lists of events arranged in chronological order.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: classical_article
-def: Works consisting of a current presentation of a previously printed seminal article marking a milestone in the history of medicine or science. It is usually accompanied by introductory remarks heralding its reprinting, often on the anniversary of its original publication or on an anniversary of the author's birth or death. It is usually reprinted in full, with complete bibliographical reference to the original appearance.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: clinical_conference
-def: Work that consists of a conference of physicians on their observations of a patient at the bedside, regarding the physical state, laboratory and other diagnostic findings, clinical manifestations, results of current therapy, etc. A clinical conference usually ends with a confirmation or correction of clinical findings by a pathological diagnosis performed by a pathologist. "Clinical conference" is often referred to as a "clinico-pathological conference."
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: clinical_trial
-def: Work that is the report of a pre-planned clinical study of the safety, efficacy, or optimum dosage schedule of one or more diagnostic, therapeutic, or prophylactic drugs, devices, or techniques in humans selected according to predetermined criteria of eligibility and observed for predefined evidence of favorable and unfavorable effects. While most clinical trials concern humans, this publication type may be used for clinical veterinary articles meeting the requisites for humans. Specific headings for specific types and phases of clinical trials are also available.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: clinical_trial_phase_I
-def: Work that is the report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques based on a small number of healthy persons and conducted over the period of about a year in either the United States or a foreign country.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-synonym: "Clinical Trial, Phase I" EXACT []
-
-[Term]
-id: TPUB:0000100
-name: clinical_trial_phase_II
-def: Work that is a report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques based on several hundred volunteers, including a limited number of patients, and conducted over a period of about two years in either the United States or a foreign country.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-synonym: "Clinical Trial, Phase II" EXACT []
-
-[Term]
-id: TPUB:0000100
-name: clinical_trial_phase_III
-def: Work that is a report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques after phase II trials. A large enough group of patients is studied and closely monitored by physicians for adverse response to long-term exposure, over a period of about three years in either the United States or a foreign country.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-synonym: "Clinical Trial, Phase III" EXACT []
-
-[Term]
-id: TPUB:0000100
-name: clinical_trial_phase_IV
-def: Work that is a report of a planned post-marketing study of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques that have been approved for general sale after clinical trials, phases I, II, and III. These studies, conducted in the United States or a foreign country, often garner additional data about the safety and efficacy of a product.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-synonym: "Clinical Trial, Phase IV" EXACT []
-
-[Term]
-id: TPUB:0000100
-name: collected_correspondence
-def: Works consisting of collected letters by or about a person or on a subject.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: collected_works
-def: Works consisting of collections of previously published works.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: collections
-def: Works that consist of collections of objects.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: comment
-def: Work consisting of a critical or explanatory note written to discuss, support, or dispute an article or other presentation previously published. It may take the form of an article, letter, editorial, etc. It appears in publications under a variety of names: comment, commentary, editorial comment, viewpoint, etc.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: comparative_study
-def: Comparison of outcomes, results, responses, etc for different techniques, therapeutic approaches or other inputs.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: congresses
-def: Published records of the papers delivered at or issued on the occasion of individual congresses, symposia, and meetings; abstracts of papers delivered at such congresses; reports of the officers and delegates of such congresses; combinations of the foregoing; or proceedings of the conference of a society if they are not limited to matters of internal organization.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: consensus_development_conference
-def: A work that consists of summary statements representing the majority and current agreement of physicians, scientists, and other professionals meeting to reach a consensus on a selected subject.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: controlled_clinical_trial
-def: Work consisting of a clinical trial involving one or more test treatments, at least one control treatment, specified outcome measures for evaluating the studied intervention, and a bias-free method for assigning patients to the test treatment. The treatment may be drugs, devices, or procedures studied for diagnostic, therapeutic, or prophylactic effectiveness. Control measures include placebos, active medicine, no-treatment, dosage forms and regimens, historical comparisons, etc. When randomization using mathematical techniques, such as the use of a random numbers table, is employed to assign patients to test or control treatments, the trial is characterized as a RANDOMIZED CONTROLLED TRIAL.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: cookbooks
-def: Collections of recipes or instructions for preparation of food and organization of meals.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: corrected_and_republished_article
-def: Work that is the republication of an article to correct, amplify, or restore text and data of the originally published article.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: database
-def: Work consisting of a structured file of information or a set of logically related data stored and retrieved using computer-based means.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: diaries
-def: Works consisting of records, usually private, of writers' experiences, observations, feelings, attitudes, etc. They may also be works marked in calendar order in which to note appointments and the like. (From Random House Unabridged Dictionary, 2d ed)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: dictionary
-def: A reference book containing a list of words - usually in alphabetical order - giving information about form, pronunciation, etymology, grammar, and meaning. A foreign-language dictionary is an alphabetical list of words of one language with their meaning and equivalents in another language.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: directory
-def: Work consisting of an alphabetical or classified list of names, organizations, subjects, etc., giving usually titles, addresses, affiliations, and other professional data.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: documentary
-def: Works consisting of films, videos, and programs which depict actual persons or actual events. They do not include frank historical re-creations and do not attempt to judge the truth of the depiction in a film purporting to be factual or documentary in character. (From Moving Image Materials: Genre Terms, 1988)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-synonym: "Documentaries and Factual Films" EXACT []
-
-[Term]
-id: TPUB:0000100
-name: drawings
-def: Works consisting of graphic representations of objects or ideas by lines.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: duplicate_publication
-def: Work consisting of an article or book of identical or nearly identical material published simultaneously or successively to material previously published elsewhere, without acknowledgment of the prior publication.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: editorial
-def: Work consisting of a statement of the opinions, beliefs, and policy of the editor or publisher of a journal, usually on current matters of medical or scientific significance to the medical community or society at large. The editorials published by editors of journals representing the official organ of a society or organization are generally substantive.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: electronic_supplementary_materials
-def: Supporting content or information, such as animation, datasets, multimedia files, video, movies, audio files, text files, or software, which is submitted for publication in an online journal or an online edition of a journal. This information may be referenced in the text of the article with a link to the supplementary data provided. CATALOG: do not use
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: encyclopedias
-def: Works containing informational articles on subjects in every field of knowledge, usually arranged in alphabetical order, or a similar work limited to a special field or subject. (From The ALA Glossary of Library and Information Science, 1983)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: ephemera
-def: Works consisting of transient everyday items, usually printed on paper, that are produced for a specific limited use and then often thrown away. (From Genre Terms: A Thesaurus for Use in Rare Book and Special Collections Cataloguing, 2d ed & The ALA Glossary of Library and Information Science, 1983)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: essays
-def: Works consisting of collections of papers or interpretive literary compositions not previously published.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: evaluation_studies
-def: Works consisting of studies determining the effectiveness or utility of processes, personnel, and equipment.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: examination_questions
-def: Works consisting of compilations of questions and answers pertaining to a particular subject, used for study and review.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: exhibitions
-def: Public displays or items representative of a given subject.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: festschrift
-def: Work consisting of a collection of essays or other writings contributed by students, teachers, colleagues, and associates to honor a person or institution, usually on the occasion of an anniversary celebration or other event of importance.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: fictional_works
-def: Works consisting of creative writing, not presented as factual.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: forms
-def: Works consisting of or containing a substantial number of blank forms.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: formularies
-def: Works that consist of lists of drugs or collections of recipes, formulas, and prescriptions for the compounding of medicinal preparations.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: government_publications
-def: Works consisting of documents issued by local, regional, or national governments or by their agencies or subdivisions.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: guidebooks
-def: Works consisting of publications for travelers that give information about a city, region, or country, or similar handbooks about buildings, museums, etc. (The ALA Glossary of Library and Information Science, 1983)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: guideline
-def: Work consisting of a set of statements, directions, or principles presenting current or future rules or policy. Guidelines may be developed by government agencies at any level, institutions, organizations such as professional societies or governing boards, or by the convening of expert panels. The text may be cursive or in outline form, but it is generally a comprehensive guide to problems and approaches in any discipline or activity. This concept relates to the general conduct and administration of health care activities rather than to specific decisions for a particular clinical condition. For that aspect, PRACTICE GUIDELINE is available.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: handbooks
-def: Works consisting of concise reference works in which facts and information pertaining to a certain subject or field are arranged for ready reference and consultation rather than for continuous reading and study.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: herbals
-def: Works such as books on herbs or plants usually describing their medicinal value. (Random House Unabridged Dictionary, 2d ed)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: historical_article
-def: An article or portion of an article giving an account of past events or circumstances significant in a field of study, a profession, a discovery, an invention, etc. The concept of history is very wide, ranging from the dawn of time to the present. This publication type is often checked in conjunction with BIOGRAPHY.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: humor
-def: Works consisting of jokes and facetiae relating to a subject.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: in_vitro
-def: Studies using excised tissues.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: incunabula
-def: Books printed before 1501.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
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-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
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-def: Works consisting of nonfiction films and video designed to teach, instruct, or train. (From Moving Image Materials: Genre Terms, 1988)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
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-def: Video recordings or other files in which the progress of the instruction or content is determined by user response.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
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-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
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-def: Prefactory summary to a special issue or section of a journal devoted to a specific topic. This introductory text can be of varying length and substance.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
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-def: The predominant publication type for articles and other items indexed for NLM databases.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
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-def: Works produced for children through age 15 or through the ninth grade.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: laboratory_manuals
-def: Works containing concise background information and directions for activities, including conducting experiments or diagnostic tests in the laboratory.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: lecture_notes
-def: Works consisting of notes taken at the delivery or reading of a speech before an audience or class, usually given to instruct. (From Random House Unabridged Dictionary, 2d ed)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: lectures
-def: Works consisting of speeches read or delivered before an audience or class, especially for instruction or to set forth some subject. They are differentiated from ADDRESSES [PUBLICATION TYPE] which are less didactic and more informational, entertaining, inspirational, or polemic. (From Random House Unabridged Dictionary, 2d ed)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: legal_cases
-def: Works consisting of collections of law reports or the published reports of decided cases and documents or filings related to those cases.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: legislation
-def: Works consisting of the text of proposed or enacted legislation that may be in the form of bills, laws, statutes, ordinances, or government regulations.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: letter
-def: Work consisting of written or printed communication between individuals or between persons and representatives of corporate bodies. The correspondence may be personal or professional. In medical and other scientific publications the letter is usually from one or more authors to the editor of the journal or book publishing the item being commented upon or discussed. LETTER is often accompanied by COMMENT.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: manuscripts
-def: Works prepared by hand including handwritten or typescript drafts of pre-publication papers or works not otherwise reproduced in multiple copies.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: maps
-def: Works consisting of representations, normally to scale and on a flat medium, of a selection of material or abstract features on the surface of the earth. They may be used also in delineating the heavens and celestial bodies. (From Anglo-American Cataloguing Rules, 2d ed, p619)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: meeting_abstracts
-def: For individual abstracts of presentations at meetings, congresses, conferences, symposia, colloquia, seminars, workshops, round tables, and other professional gatherings.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: meta_analysis
-def: Works consisting of studies using a quantitative method of combining the results of independent studies (usually drawn from the published literature) and synthesizing summaries and conclusions which may be used to evaluate therapeutic effectiveness, plan new studies, etc. It is often an overview of clinical trials. It is usually called a meta-analysis by the author or sponsoring body and should be differentiated from reviews of literature.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: monograph
-def: Work that is any publication that is not a serial or integrating resource. In cataloging usage, It is usually on a single subject or related subjects and is complete in itself, whether constructed of chapters, sections, or parts. While any article encountered in indexing journals can be, strictly speaking, a monograph, as a publication type, a monograph will refer to a cataloging item.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: multicenter_study
-def: Work consisting of a controlled study executed by several cooperating institutions.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: news
-def: Works consisting of an announcement or statement of recent or current events of new data and matters of interest in the field of medicine or science. In some publications, such as "Nature" or "Science," the news reports are substantively written and herald medical and scientific data of vital or controversial importance.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: newspaper_article
-def: Work consisting of a news item appearing in a general-interest newspaper or other general news periodical, containing information of current and timely interest in the field of medicine or science. This publication type should not be confused with NEWS Publication Type, reserved for news reports published in various medical or other scientific journals, such as "Nature".
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: nurses_instruction
-def: Works consisting of materials developed for a nursing audience.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-synonym: "Nurses' Instruction" EXACT []
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-[Term]
-id: TPUB:0000100
-name: outlines
-def: Works consisting of brief statements of the principal elements of a subject, usually arranged by heads and subheads.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: overall
-def: A single citation covering papers or abstracts presented at a meeting. The publication type may be used for a single citation with or without the additional indexing or cataloging of individual papers. The individual papers, however, are not labeled OVERALL.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: patents
-def: Works consisting of documents granted by a government giving exclusive rights to an inventor or assignee to manufacture, use, or sell an invention for a certain number of years.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: patient_education_handout
-def: Works consisting of a handout or self-contained informative material used to explain a procedure or a condition or the contents of a specific article in a biomedical journal and written in non-technical language for the patient or consumer.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: periodical_index
-def: Work consisting of a subject approach to the contents of a periodical issuing an annual, biennial, quinquennial, decennial, etc., index. The heading is used for the overall body of articles published by a periodical in the same sense that BIBLIOGRAPHY is useful when published as a single article.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: periodicals
-def: Publications intended to be issued on an ongoing basis, generally more frequently than annually, containing separate articles, stories, or writings.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: personal_narratives
-def: Works consisting of accounts of individual experience in relation to a particular field or of participation in related activities.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: pharmacopoeias
-def: Authoritative works containing lists of drugs and preparations, their description, formulation, analytic composition, main chemical properties, standards for strength, purity, and dosage, chemical tests for determining identity, etc. They have the status of a standard.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: photographs
-def: Still images produced from radiation-sensitive materials (sensitive to light, electron beams, or nuclear radiation), generally by means of the chemical action of light on a sensitive film, paper, glass, or metal. Photographs may be positive or negative, opaque or transparent.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: phrases
-def: Works consisting of common terms, phrases, idioms, and typical conversations, e.g., between health professional and patients. These are often intended for use by non-native speakers of a language.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: pictorial_works
-def: Works consisting exclusively or mainly of pictures but not technical drawings.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: poetry
-def: Works that consist of literary and oral genre expressing meaning via symbolism and following formal or informal patterns.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: popular_works
-def: Works written for non-professional or lay audiences.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: portraits
-def: Works consisting of graphic representations, especially of the face, of real persons, usually posed, living or dead. They are pictures whose purpose is the portrayal of an individual or group of individuals, not pictures which merely include people as part of an event or scene. (From Thesaurus for Graphic Materials II, p540, 1995)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: Postcards
-def: Cards on which a message may be written or printed for mailing without an envelope. Art & Architectural Thesaurus Online www.getty.edu/research/conducting_research/vocabularies/aat/ accessed 12/18/2008
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: posters
-def: Works consisting of single or multi-sheet notices made to attract attention to events, activities, causes, goods, or services. They are for posting, usually in a public place and are chiefly pictorial. They are intended to make an immediate impression from a distance. Posters do not include poster presentations at conferences and meetings. (From Thesaurus for Graphic Materials II: Genre and Physical Characteristic Headings, 1995)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: practice_guideline
-def: Work consisting of a set of directions or principles to assist the health care practitioner with patient care decisions about appropriate diagnostic, therapeutic, or other clinical procedures for specific clinical circumstances. Practice guidelines may be developed by government agencies at any level, institutions, organizations such as professional societies or governing boards, or by the convening of expert panels. They can provide a foundation for assessing and evaluating the quality and effectiveness of health care in terms of measuring improved health, reduction of variation in services or procedures performed, and reduction of variation in outcomes of health care delivered.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: price_lists
-def: Works consisting of lists giving the prices of items for sale, including drugs, equipment, books, etc. Price lists are less detailed than catalogs and not as long.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: problems_and_exercises
-def: Works consisting of collections of practice questions and drills, generally for instructional or review use.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: programmed_instruction
-def: Works consisting of sequenced self-correction texts.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: programs
-def: Works consisting of lists of the events, pieces, performers, speakers, etc., of an entertainment, ceremony, or the like. (From: Genre Terms: A Thesaurus for Use in Rare Book and Special Collections Cataloging, 2d ed)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: prospectuses
-def: Works consisting of advertisements separately printed and distributed by a publisher to describe and solicit orders for a recent or forthcoming publication. In the case of books, they may include sample pages. (From: ALA Glossary of Library and Information Science, 1983)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
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-def: Specific parts of publications.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
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-def: Specific genre of publication.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
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-name: published_erratum
-def: Work consisting of an acknowledgment of an error, issued by a publisher, editor, or author. It customarily cites the source where the error occurred, giving complete bibliographic data for retrieval. In the case of books and monographs, author, title, imprint, paging, and other helpful references will be given; in the case of journal articles, the author, title, paging, and journal reference will be shown. An erratum notice is variously cited as Errata or Corrigenda.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: randomized_controlled_trial
-def: Work consisting of a clinical trial that involves at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: resource_guides
-def: Works listing and describing various sources of information, from multiple media or in different formats, on a given subject.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: retracted_publication
-def: Work consisting of the designation of an article or book as retracted in whole or in part by an author or authors or an authorized representative. It identifies a citation previously published and now retracted through a formal issuance from the author, publisher, or other authorized agent, and is distinguished from RETRACTION OF PUBLICATION, which identifies the citation retracting the original published item.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
-
-[Term]
-id: TPUB:0000100
-name: retraction_of_publication
-def: Work consisting of a statement issued by one or more authors of an article or a book, withdrawing or disavowing acknowledgment of their participation in performing research or writing the results of their study. In indexing, the retraction is sent to the editor of the publication in which the article appeared and is published under the rubric "retraction" or in the form of a letter. This publication type designates the author's statement of retraction: it should be differentiated from RETRACTED PUBLICATION which labels the retracted publication.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: review
-def: An article or book published after examination of published material on a subject. It may be comprehensive to various degrees and the time range of material scrutinized may be broad or narrow, but the reviews most often desired are reviews of the current literature. The textual material examined may be equally broad and can encompass, in medicine specifically, clinical material as well as experimental research or case reports. State-of-the-art reviews tend to address more current matters. A review of the literature must be differentiated from HISTORICAL ARTICLE on the same subject, but a review of historical literature is also within the scope of this publication type.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: scientific_integrity_review
-def: Work consisting of reports by the United States Office of Research Integrity, identifying questionable research published in articles or books. Notification of the questionable data is carried in the NIH Guide for Grants and Contracts.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: statistics
-def: Works consisting of presentations of numerical data on particular subjects.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: support_of_research
-def: Organizational source for funding of research activity.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
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-def: Presentations of nonstatistical data in tabular form.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: technical_report
-def: Work consisting of a formal report giving details of the investigation and results of a medical or other scientific problem. When issued by a government agency or comparable official body, its contents may be classified, unclassified, or declassified with regard to security clearance. This publication type may also cover a scientific paper or article that records the current state or current position of scientific research and development. If so labeled by the editor or publisher, this publication type may be properly used for journal articles.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: terminology
-def: Work consisting of lists of the technical terms or expressions used in a specific field. These lists may or may not be formally adopted or sanctioned by usage.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: textbooks
-def: Books intended for use in the study of specific subjects, containing systematic presentation of the principles and essential knowledge of the subjects.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: twin_study
-def: Work consisting of reporting using a method of detecting genetic causes in human traits and genetic factors in behavior using sets of twins.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: unedited_footage
-def: Work consisting of untitled raw motion picture and video footage which has not been edited or assembled into a finished work. (From: Moving Image Materials: Genre Terms, 1988)
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: union_lists
-def: Works consisting of records of the holdings or items owned by two or more libraries.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: unpublished_works
-def: Works that have not been formally published.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: validation_studies
-def: Works consisting of research using processes by which the reliability and relevance of a procedure for a specific purpose are established.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: video_audio_media
-def: Used with articles which include video files or clips, or for articles which are entirely video.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-[Term]
-id: TPUB:0000100
-name: webcasts
-def: Content from transmission of live or pre-recorded audio or video via connection or download from the INTERNET.
-is_a: TPUB:0000015 ! publication_type
-namespace: MeSH_publication_type
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-range: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#Author  ! Author
-
-[Typedef]
-id: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#isDescribedBy
-domain: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#Project  ! Project
-range: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#Publication  ! Publication
-
-[Typedef]
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-domain: p:Person 
-range: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#Journal  ! Journal
-
-[Typedef]
-id: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#isKeywordOf
-domain: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#Keyword  ! Keyword
-range: __/home/obo/galaxy_dist/database/files/000/dataset_219.dat#__Description4 
-
-[Typedef]
-id: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#isOrganizerOf
-domain: p:Organization 
-range: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#Event  ! Event
-
-[Typedef]
-id: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#isPartOf
-domain: __/home/obo/galaxy_dist/database/files/000/dataset_219.dat#__Description6 
-range: __/home/obo/galaxy_dist/database/files/000/dataset_219.dat#__Description7 
-
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-domain: __/home/obo/galaxy_dist/database/files/000/dataset_219.dat#__Description13 
-range: p:Organization 
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-[Typedef]
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-domain: p:Organization 
-range: __/home/obo/galaxy_dist/database/files/000/dataset_219.dat#__Description12 
-
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-domain: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#Publication  ! Publication
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-
-[Typedef]
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-range: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#Event  ! Event
-
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-domain: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#IndexTerm  ! Index term
-range: __/home/obo/galaxy_dist/database/files/000/dataset_219.dat#__Description10 
-
-[Typedef]
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-domain: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#Publication  ! Publication
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-
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-
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-

tripal_pub/tpub.obo

@@ -1293,18 +1293,23 @@ name: Author List
 relationship: part_of TPUB:0000037 ! Publication Details
 
 [Term]
-id: TPUB0000241
+id: TPUB:0000241
 name: English Abstract
 subset: MeSH_Publication_Type
 is_a: TPUB:0000015 ! Publication Type
 
 [Term]
-id: TPUB0000242
+id: TPUB:0000242
 name: Meta-Analysis
 def: Works consisting of studies using a quantitative method of combining the results of independent studies (usually drawn from the published literature) and synthesizing summaries and conclusions which may be used to evaluate therapeutic effectiveness, plan new studies, etc. It is often an overview of clinical trials. It is usually called a meta-analysis by the author or sponsoring body and should be differentiated from reviews of literature.
 subset: MeSH_Publication_Type
 is_a: TPUB:0000015 ! Publication Type
 
+[Term]
+id: TPUB:0000243
+name: Volume Title
+relationship: part_of TPUB:0000037 ! Publication Details
+
 [Typedef]
 id: is_a
 name: is a

tripal_pub/tripal_pub.module

@@ -4,6 +4,7 @@ require_once "api/tripal_pub.api.inc";
 require_once "includes/tripal_pub.admin.inc";
 require_once "includes/pubmed.inc";
 require_once "includes/pub_sync.inc";
+require_once "includes/pub_form.inc";
 
 /**
  * @file
@@ -117,6 +118,21 @@ function tripal_pub_menu() {
     'type ' => MENU_CALLBACK,
   );
  
+  $items['tripal_pub/properties/add/%'] = array(    
+    'page callback' => 'tripal_pub_property_add',
+    'page arguments' => array(3),
+    'access arguments' => array('edit chado_pub content'),
+    'type ' => MENU_CALLBACK,
+  );
+  
+  $items['tripal_pub/properties/minus/%'] = array(    
+    'page callback' => 'tripal_pub_property_delete',
+    'page arguments' => array(3),
+    'access arguments' => array('edit chado_pub content'),
+    'type ' => MENU_CALLBACK,
+  );
+  
+  
   return $items;
 }
 
@@ -150,6 +166,9 @@ function tripal_pub_theme() {
     'tripal_pub_importer_setup_form' => array(
        'arguments' => array('form'),
     ),
+    'chado_pub_node_form' => array(
+       'arguments' => array('form'),
+    ),
     'tripal_pub_admin' => array(
       'template' => 'tripal_pub_admin',  
       'arguments' =>  array(NULL),  
@@ -217,134 +236,7 @@ function chado_pub_access($op, $node, $account ) {
 }
 
 
-/**
- * Implementation of tripal_pub_form().
- *
- *
- *
- *  @parm &$node
- *    The node that is created when the database is initialized
- *
- *  @parm $form_state
- *    The state of the form, that has the user entered information that is neccessary for, setting
- *    up the database tables for the publication
- *
- *  @return $form
- *    The information that was enterd allong with
- *
- */
-function chado_pub_form(&$node, $form_state) {
-
-  $type = node_get_types('type', $node);
 
-  $form['pub_id'] = array(
-    '#type' => 'hidden',
-    '#value' => (isset($node->pub_id)) ? $node->pub_id->pub_id : NULL ,
-  );
-  
-  $sql = "
-    SELECT CVTS.cvterm_id, CVTS.name
-    FROM {cvtermpath} CVTP
-      INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
-      INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
-      INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
-    WHERE CV.name = 'tripal_pub' and CVTO.name = 'Publication Type'
-    ORDER BY CVTS.name ASC 
-  ";
-  $results = chado_query($sql);
-  $pub_types = array();
-  $default_type = '';
-  while ($pub_type = db_fetch_object($results)) {
-    $pub_types[$pub_type->cvterm_id] = $pub_type->name;
-    if (strcmp($pub_type->name,"Journal Article") == 0) {
-      $default_type = $pub_type->cvterm_id;
-    }
-  }
-  $form['type_id'] = array(
-    '#type' => 'select',
-    '#title' => t('Publication Type'),
-    '#options' => $pub_types,
-    '#required' => TRUE,
-    '#default_value' => isset($node->pub_id->type_id) ? $node->pub_id->type_id : $default_type,
-  );
-  
-  // Article Title.
-  $form['title'] = array(
-    '#type' => 'textfield',
-    '#title' => check_plain($type->title_label),
-    '#default_value' => $node->title,
-    '#required' => TRUE,
-  );
-  
-  $form['volume'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Volume'),
-    '#default_value' => isset($node->pub_id->volume) ? $node->pub_id->volume : ''
-  );
-  
-  $form['volumetitle'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Volume Title'),
-    '#description' => t('Title of part if one of a series.'),
-    '#default_value' => isset($node->pub_id->volumetitle) ? $node->pub_id->volumetitle : ''
-  );
-  
-  $form['series_name'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Series Name'),
-    '#description' => t('Full name of (journal) series.'),
-    '#default_value' => isset($node->pub_id->series_name) ? $node->pub_id->series_name : ''
-  );
-
-  $form['issue'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Issue'),
-    '#default_value' => isset($node->pub_id->issue) ? $node->pub_id->issue : ''
-  );
-
-  $form['pyear'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Publication Year'),
-    '#default_value' => isset($node->pub_id->pyear) ? $node->pub_id->pyear : ''
-  );
-
-  $form['pages'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Pages'),
-    '#description' => t('Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'),
-    '#default_value' => isset($node->pub_id->pages) ? $node->pub_id->pages : ''
-  );
-
-  $form['miniref'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Mini-Ref'),
-    '#required' => FALSE,
-    '#default_value' => isset($node->pub_id->miniref) ? $node->pub_id->miniref : ''
-  );
-
-  $form['publisher'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Publisher Name'),
-    '#required' => FALSE,
-    '#default_value' => isset($node->pub_id->publisher) ? $node->pub_id->publisher : ''
-  );
-
-  $form['pubplace'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Place of Publication'),
-    '#required' => FALSE,
-    '#default_value' => isset($node->pub_id->pubplace) ? $node->pub_id->pubplace  : ''
-  );
-  
-  $form['is_obsolete'] = array(
-    '#type' => 'checkbox',
-    '#title' => t('Is Obsolete? (Check for Yes)'),
-    '#required' => TRUE,
-    '#default_value' => isset($node->pub_id->is_obsolete) ? $node->pub_id->is_obsolete : FALSE
-  );
-  return $form;
-
-}
 
 
 /**