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obi-ontology / obi

The Ontology for Biomedical Investigations
http://obi-ontology.org
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terms without curation_status #40

Closed obi-bot closed 7 years ago

obi-bot commented 16 years ago

Transformation-ML "Transformation-ML" report_display_element "report display element" OBI_48 "liquid_chromatography_instrument" text_based_digital_entity "text based digital entity" is_manufactured_by "is_manufactured_by" OBI_10000003 "incubator" information_content_entity "information content entity" OBI_155 "disease" OBI_191 "gaseous_state" fluorescent_reporter_intensity "fluorescent reporter intensity" narrative_object "narrative object" OBI_10000008 "supernatant_collection_system_harvesting_frame" ready_for_release "ready for release" OBI_354 "disease_course" inputs_data "inputs_data" metadata_complete "metadata complete" metadata_incomplete "metadata incomplete" OBI_22 "input_role" OBI_400148 "DNA_microarray" ACS "ACS" OBI_10000005 "paper_filter" is_instrument_for "is_instrument_for" has_input "has_input" OBI_50 "platform" OBI_72 "parameter_value_application" list-mode_data_file "list-mode data file" OBI_76 "unplanned_process_part" OBI_49 "mass_spectrometer" report_figure "report figure" eSource_document "eSource document" journal_article_content "journal article content" patent_content "patent content" OBI_137 "state" image "image" XML "XML" OBI_357 "author role" OBI_138 "in-vivo_state" Supernatant_role "supernatant role" is_reagent_in "is_reagent_in" Vector_role "vector role" OBI_254 "specimen_role" source_code_module "source code module" OBI_189 "liquid_state" electronic_case_report_form "electronic case report form" data_set "data set" is_output_of "is_output_of" pending_final_vetting "pending final vetting" OBI_270 "algorithm" parameter_threshold "parameter threshold" OBI_344 "plan" non-realizable_information_entity "non-realizable information entity" outputs_data "outputs_data" p-value "p-value" ratio_of_collected_to_emitted_light_ "ratio of collected to emitted light " measurement_unit "measurement unit" OBI_139 "frozen_state" programming_language "programming language" OBI_10000002 "gamma_counter" density_plot "density plot" OBI_52 "microarray_platform" Class_11 "evaluant" quantitative_confidence_value "quantitative confidence value" digital_document "digital document" is_input_of "is_input_of" eMedical_record "eMedical record" RDF "RDF" software_interpreter "software interpreter" Class_10 "information entity" is_proxy_for "is_proxy_for" OBI_400152 "software" OBI_278 "disease_stage" electronic_case_report_tabulation "electronic case report tabulation" OBI_10000004 "polystyrene_tube" zip "zip" analytical_cytology_data_file "analytical cytology data file" OBI_94 "material_transformation" tar "tar" fluorescence_compensation_matrix "fluorescence compensation matrix" has_output "has_output" report_of_results "report of results" investigation_results_report "investigation results report" OBI_44 "physical_document" measured_expression_level "measured expression level" OBI_305 "datum" binary_executable "binary executable" OBI_400142 "power_pack" OBI_130 "in-vitro_state" FCS "FCS" uncurated "uncurated" OBI_190 "solid_state" OBI_400147 "microarray" standard_error "standard error" _under_discussion "_under_discussion" Compensation-ML "Compensation-ML" biological_specimen_role "biological specimen role" report_graph "report graph" OBI_259 "ex-vivo_state" OBI_51 "liquid_chromatography_mass_spectrometry_platform" binary_digital_entity "binary digital entity" Gating-ML "Gating-ML" number_of_particles_in_subset "number of particles in subset" gene_list "gene list" contour_plot "contour plot" cluster "cluster" Cohort_role "cohort role" dot_plot "dot plot" digital_entity "digital entity" number_of_lost_events_electronic "number of lost events electronic" report_table "report table" utilizes_reagent "utilizes_reagent" OBI_23 "output_role" OBI_400149 "protein_microarray" OWL "OWL" number_of_lost_events_computer "number of lost events computer" utilizes_instrument "utilizes_instrument"

(sparql '(:select (?thing ?label) () (?thing :a !owl:Thing) (?thing !rdfs:label ?label) (:optional (?thing !obi:curation_status ?status)) (:filter (not (bound ?status)))) :kb kb :use-reasoner :jena :flatten t :trace "classes without curation_status")

PREFIX obi: <http://obi.sourceforge.net/ontology/OBI.owl\#&gt; PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema\#&gt; PREFIX owl: <http://www.w3.org/2002/07/owl\#&gt; SELECT ?thing ?label WHERE { ?thing a owl:Thing . ?thing rdfs:label ?label . OPTIONAL { ?thing obi:curation_status ?status . }. FILTER (!(bound(?status)))}

Reported by: alanruttenberg

Original Ticket: "obi/obi-terms/40":https://sourceforge.net/p/obi/obi-terms/40

obi-bot commented 16 years ago

Original comment by: mcourtot

obi-bot commented 16 years ago

Logged In: YES user_id=1572691 Originator: NO

cf obi-dev call 5th of March 2008: all branches have until the 9th of March to update their curation status to the new values. On Monday, we will add a default curation_status property to terms that don't have any, with curation_status level 1, i.e. uncurated. I assign the tracker to myself, but I'm sure Alan and Bill will help out as part of the general release process :-)

Original comment by: mcourtot

obi-bot commented 15 years ago

Logged In: YES user_id=1572691 Originator: NO

new list (we decided not to correct those) Query: Terms missing curation status Results: !obi:OBI_0000309 "utilizes_reagent" !owl:ObjectProperty !obi:OBI_0000308 "is_realization_of" !owl:ObjectProperty !obi:OBI_0000294 "is_concretization_of" !owl:ObjectProperty !obi:OBI_0000295 "is_input_of" !owl:ObjectProperty !obi:OBI_0000316 "has_role" !owl:ObjectProperty !obi:OBI_0000315 "inputs_data" !owl:ObjectProperty !obi:OBI_0000300 "is_realized_as" !owl:ObjectProperty !obi:OBI_0000301 "outputs_data" !owl:ObjectProperty !obi:OBI_0000314 "is_proxy_for" !owl:ObjectProperty !obi:OBI_0000313 "utilizes_device" !owl:ObjectProperty !obi:OBI_0000304 "is_manufactured_by" !owl:ObjectProperty !obi:OBI_0000307 "is_reagent_in" !owl:ObjectProperty !obi:OBI_0000306 "has_function" !owl:ObjectProperty !obi:OBI_0000293 "has_input" !owl:ObjectProperty !obi:OBI_0000297 "is_concretized_as" !owl:ObjectProperty !obi:OBI_0000299 "has_output" !owl:ObjectProperty !obi:OBI_0000298 "has_quality" !owl:ObjectProperty !obi:OBI_0000311 "is_device_for" !owl:ObjectProperty !obi:OBI_0000312 "is_output_of" !owl:ObjectProperty !obi:OBI_0000292 "has_feature_value" !owl:DatatypeProperty !obi:OBI_0000109 "vector role" !owl:Class !obi:OBI_0000212 "funder" !owl:Class !obi:OBI_0000104 "protocol application role" !owl:Class !obi:OBI_0000112 "biological specimen role" !owl:Class !obi:OBI_9999998 "label_role" !owl:Class !obi:OBI_0302711 "_move to information_content_entity" !owl:Class !obi:OBI_0200000 "data transformation" !owl:Class !obi:OBI_0000095 "number" !owl:Class !obi:OBI_0900007 "dialysis tubing function" !owl:Class !obi:OBI_0000137 "state" !owl:Class !obi:OBI_0000012 "organization_role" !owl:Class !obi:OBI_0000257 "DNA extraction" !owl:Class !obi:OBI_0000236 "_under_discussion" !owl:Class !obi:OBI_0000029 "pellet role" !owl:Class !obi:OBI_0000226 "precipitate role" !owl:Class !obi:OBI_0000259 "ex-vivo_state" !owl:Class !obi:OBI_0000334 "_to_be_fixed" !owl:Class !obi:OBI_0600049 "DNA polymerase amplification" !owl:Class !obi:OBI_9999997 "chromium_release_assay_effector_role" !owl:Class !obi:OBI_0000091 "detector reagent role" !owl:Class !obi:OBI_0000072 "parameter_value_application" !owl:Class !obi:OBI_0000138 "in-vivo_state" !owl:Class !obi:OBI_0000206 "format standard" !owl:Class !obi:OBI_0600055 "DNA cleavage, restriction analysis" !owl:Class !obi:OBI_0600005 "taking sample from organism" !owl:Class !obi:OBI_0000090 "treated role" !owl:Class !obi:OBI_9999996 "chromium_release_assay_target_role" !owl:Class !obi:OBI_0000187 "data format specification" !owl:Class !obi:OBI_0000357 "author role" !owl:Class !obi:OBI_0302710 "_move to protocol application" !owl:Class !obi:OBI_0000033 "sex_effect" !owl:Class !obi:OBI_0000155 "disease" !owl:Class !obi:OBI_0600017 "detection of label" !owl:Class !obi:OBI_0500008 "balanced incomplete block design" !owl:Class !obi:OBI_0600018 "material portioning" !owl:Class !obi:OBI_0000252 "cohort role" !owl:Class !obi:OBI_0000023 "output_role" !owl:Class !obi:OBI_0000044 "physical_document" !owl:Class !obi:OBI_0000035 "_cloning placeholder" !owl:Class !obi:OBI_0600033 "cell permeabalization" !owl:Class !obi:OBI_0000067 "evaluant" !owl:Class !obi:OBI_0000254 "specimen_role" !owl:Class !obi:OBI_0000289 "reporter_role" !owl:Class !obi:OBI_0000022 "input_role" !owl:Class !obi:OBI_0302719 "histologic preparation" !owl:Class !obi:OBI_0000034 "supernatant role" !owl:Class !obi:OBI_0302718 "?all kind ofl lavage" !owl:Class

Original comment by: mcourtot

obi-bot commented 15 years ago

OK - what do we do with those? I am not sure there is any interest in keeping that tracker item open. The list of terms missing curation status is produced at each release as part of the qc-queries. I am closing this item - we decided a while ago to not assign an uncurated status to terms missing one. This can be revised as needed, and if this is the case it will use a recently compiled list. Melanie

Original comment by: mcourtot

obi-bot commented 15 years ago

Original comment by: mcourtot