diff --git a/src/ontology/components/orcidio.owl b/src/ontology/components/orcidio.owl index d8807e1..21d6414 100644 --- a/src/ontology/components/orcidio.owl +++ b/src/ontology/components/orcidio.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2026-06-22") + +Annotation(owl:versionInfo "2026-06-25") Declaration(Class()) Declaration(NamedIndividual()) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 2852dd2..5bf92de 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2026-06-22") + +Annotation(owl:versionInfo "2026-06-25") Declaration(Class()) Declaration(Class()) @@ -278,7 +278,7 @@ AnnotationAssertion( "has broad synonym"@en) AnnotationAssertion(rdfs:label "has_broad_synonym") -# Annotation Property: (database_cross_reference) +# Annotation Property: (has cross-reference) AnnotationAssertion( "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.") AnnotationAssertion( ) @@ -1395,7 +1395,7 @@ AnnotationAssertion(rdfs:label "kina SubClassOf( ) SubClassOf( ObjectHasSelf()) -# Class: (data entity) +# Class: (data item) AnnotationAssertion( "An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) AnnotationAssertion(rdfs:label "data entity"@en) diff --git a/src/ontology/reports/basic-report.tsv b/src/ontology/reports/basic-report.tsv index a04f6ad..6ac9819 100644 --- a/src/ontology/reports/basic-report.tsv +++ b/src/ontology/reports/basic-report.tsv @@ -78,6 +78,7 @@ + "A visualization method that detects a probe conjugated to a HiLyte647 label." "Tissue made permeable by the action of glycerol" @@ -102,7 +103,6 @@ - "A method of reconstructing 3D structure by combining serial sectioning with scanning EM." @@ -136,7 +136,6 @@ "A visualization method that detects a cyan fluorescent protein tag." - "Cryogenic serial block-face scanning electron microscopy is a volumetric imaging technique in which the surface of a biological specimen preserved in its near-native, vitrified state is imaged by a scanning electron microscope, then ablated by a focused ion beam (FIB-SEM) to reveal a new surface, enabling three-dimensional ultrastructural reconstruction of cells and tissues without the artifacts introduced by chemical fixation or resin embedding." "Tomography using X-ray illumination." @@ -182,6 +181,7 @@ "The inelastic scattering of photons caused by interaction with matter." + "A visualization method that detects proteins labeled with the mNeonGreen fluorescent protein tag from Branchiostoma lanceolatum." @@ -247,10 +247,12 @@ + "An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en "Fully hydrated tissue rapidly frozen to produce vitrified water, and maintained continuously below the glass transition temperature of water (approximately -137 deg C" "A visualization method that detects a protein self-labelled with a SNAP-tag. A SNAP-tag is an engineered version of the mammalian enzyme AGT that can covalently bind O6-benzylguanine-based ligands." + @@ -263,6 +265,7 @@ "Methods and devices used for capturing an image of a real object; distinct from images created by artwork" + "Cryogenic focused ion beam scanning electron microscopy is a volumetric imaging technique in which the surface of a biological specimen preserved in its near-native, vitrified state is imaged by a scanning electron microscope, then ablated by a focused ion beam (FIB-SEM) to reveal a new surface, enabling three-dimensional ultrastructural reconstruction of cells and tissues without the artifacts introduced by chemical fixation or resin embedding." @@ -305,6 +308,7 @@ "Fluorophore with ex/em 589/615" "A visualization method that detects proteins labeled with the mTurquoise fluorescent protein tag from Aequorea victoria." + "A method that images the phototoxicity of a fluorophore." "Illumination restricted to angles that exceed the acceptance angle of the image-forming lens" @@ -320,11 +324,13 @@ + "A visualization method that detects a probe conjugated to a Cy3B label." + "A sample preparation method allowing the image of stably transfected cells." @@ -341,6 +347,7 @@ + "The staining method involves application of hemalum, which is a complex formed from aluminium ions and oxidized haematoxylin. This colors nuclei of cells (and a few other objects, such as keratohyalin granules) blue. The staining of nuclei by hemalum does not require the presence of DNA and is probably due to binding of the dye-metal complex to arginine-rich basic nucleoproteins such as histones. The mechanism is different from that of nuclear staining by basic (cationic) dyes such as thionine or toluidine blue. Staining by basic dyes is prevented by chemical or enzymatic extraction of nucleic acids. Such extractions do not prevent staining of nuclei by hemalum." "http://en.wikipedia.org/wiki/X-ray_microscope" @@ -415,6 +422,7 @@ "Illumination by multiple points of light simultaneously" "Structured illumination used at sufficiently high power to cause significant ground-state depletion of the imaged fluorophore, thus allowing for non-linear resolution enhancement" "A visualization method that detects a far-red fluorescent protein tag." + "A sample preparation method allowing the imaging of adherent living cells." @@ -445,6 +453,7 @@ "A mode of fluorescence microscopy where the entire observed field is illuminated." "Methods of visualization that differentiate between different regions or surfaces of the specimen based on contiguity" + "A method of reconstructing 3D structure by combining in-situ serial sectioning with scanning EM." "Illumination used for the purpose of inducing some observable change in the specimen during the course of an imaging session. This illumination may or may not be the same as the illumination used for imaging. Typically used in conjunction with live-cell imaging" "A form of transmission electron microscopy in which the specimen is maintained in a vitrified state at cryogenic temperature throughout imaging. The specimen is rapidly frozen to preserve its native structure in amorphous ice, avoiding the artefacts associated with chemical fixation, dehydration, and staining. Imaging is performed with the specimen held at cryogenic temperature in a transmission electron microscope." @@ -556,6 +565,7 @@ + "A visualization method that detects the SR2200 dye, typically used to stain cell walls." "A fluorescence microscopy method in which the image contrast is derived from the fluorescence lifetime at each point in a two-dimensional image and not the local concentration and/or intensity of the fluorophore." @@ -580,6 +590,7 @@ + "A visualization method that detects the natural fluorescence emitted by endogenous biological structures or compounds." "Illumination and detection via a thin slit" @@ -596,7 +607,6 @@ "Imaged formed using electrons undergoing elastic scattering at very high angles, with emission of characteristic X-rays" - "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en @@ -658,6 +668,7 @@ "Illumination at angles less than the acceptance angle of the image-forming lens is attenuated by a filter to give a colored background of unscattered light; higher angle illumination may be filtered to give a contrasting color" "A method of reconstructing 3D structure by combining focussed ion beam milling to remove sucessive layers from a sample block with scanning EM to image the exposed surface between each milling step." + "A method that images the photobleaching of a fluorophore." "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en diff --git a/src/ontology/reports/class-count-by-prefix.tsv b/src/ontology/reports/class-count-by-prefix.tsv index 1b5aae2..7091082 100644 --- a/src/ontology/reports/class-count-by-prefix.tsv +++ b/src/ontology/reports/class-count-by-prefix.tsv @@ -2,6 +2,7 @@ "IAO" 6 "BFO" 13 "GO" 3 -"FBbi" 653 +"NCBITaxon" 1 +"FBbi" 663 "UBERON" 1 "PATO" 1 diff --git a/src/ontology/reports/edges.tsv b/src/ontology/reports/edges.tsv index 41a57b6..02b2281 100644 --- a/src/ontology/reports/edges.tsv +++ b/src/ontology/reports/edges.tsv @@ -2,10 +2,10 @@ - - + + @@ -17,14 +17,14 @@ - + - + @@ -41,6 +41,7 @@ + @@ -83,6 +84,7 @@ + @@ -190,6 +192,7 @@ + @@ -221,6 +224,7 @@ + @@ -252,6 +256,7 @@ + @@ -294,12 +299,14 @@ + + @@ -344,6 +351,7 @@ + @@ -444,6 +452,7 @@ + @@ -618,6 +627,7 @@ + diff --git a/src/ontology/reports/synonyms.tsv b/src/ontology/reports/synonyms.tsv index add5b01..46fbb2d 100644 --- a/src/ontology/reports/synonyms.tsv +++ b/src/ontology/reports/synonyms.tsv @@ -67,10 +67,10 @@ "eosin" "obsolete primary antibody-fluorescein isothiocyanate" "SYTO Red" - "silicon intensified target tube (SIT)" "stimulated emission depletion (STED)" "free hand graphic" "obsolete secondary antibody-horseradish peroxidase, 3,3'-diaminobenzidine" + "silicon intensified target tube (SIT)" "Alexa Fluor 633" "pulsed illumination" "cationic colloidal gold" @@ -131,6 +131,7 @@ "alpha-bungarotoxin" "PA-GFP" "tissue in plastic embedment" + "Cy3B" "graphite pencil graphic" "glycerol permeabilized" "retardance" @@ -252,6 +253,7 @@ "Kusabira OrangeFP2" "orientation-independent polarization microscopy" "non-immunological protein probe" + "stably transfected cells" "colored pencil graphic" "vizualization of label conjugated to probe" "dispersed cells in vitro" @@ -266,6 +268,7 @@ "SiriusFP" "Medium-FT" "unfixed tissue" + "adherent live cells" "charcoal pencil graphic" "refractive index" "detection of X-ray photons" @@ -275,11 +278,13 @@ "obsolete dummy term" "[35]S" "FLIP" + "fluorescent protein derived from Branchiostoma" "acridine homodimer" "montage" "mRFP1" "mScarlet" "vibratome-sectioned tissue" + "mNeonGreen" "illumination by acoustic waves" "obsolete primary antibody-horseradish peroxidase, 4-chloro-1-naphthol" "detection of UV/visible/IR photons" @@ -375,11 +380,12 @@ "probe for lysosomes" "tissue in polyester wax embedment" "single-spot confocal microscopy" - "tdTomatoFP" "sequence-specific nucleic acid probe" + "tdTomatoFP" "Wiener filter" "intermediate voltage electron microscopy (IVEM)" "AzuriteFP" + "phototoxicity" "line art graphic" "sub-nanosecond time-resolved fluorescence emission)" "ZsYellowFP" @@ -439,7 +445,7 @@ "obsolete fluoroscein labeled RNA probe" "mPlumFP" "blue fluorescent protein from Aequorea" - "focussed ion beam scanning electron microscopy (FIB-SEM)" + "focused ion beam scanning electron microscopy" "DNA probe" "methyl green" "Phaseolus vulgaris lectin PHA-L)" @@ -482,6 +488,7 @@ "methanol fixed tissue" "uranium compound" "genetically encoded enzyme" + "green fluorescent protein from Branchiostoma" "Rheinberg illumination" "obsolete secondary antibody-phosphatase, Naphthol-AS-BI-phosphate" "obsolete X-rhodamine tubulin fill" @@ -541,7 +548,8 @@ "non-specific protein affinity" "DsRed-ES FP" "osmium tetroxide fixed tissue" - "cryogenic serial block face scanning electron microscopy" + "photobleaching" + "cryogenic focused ion beam scanning electron microscopy" "wheat germ agglutinin" "saponin permeabilized" "genetically encoded biotin tag" @@ -640,7 +648,7 @@ "cryogenic scanning electron microscopy" "fluorescence lifetime imaging microscopy" "obsolete [32]P labeled RNA probe" - "serial block face SEM (SBFSEM)" + "serial block face scanning electron microscopy" "intensified CCD (ICCD)" "differences in fluorescence lifetime" "probe for endoplasmic reticulum" @@ -653,6 +661,7 @@ "linear method" "freeze-substituted tissue" "DsRed-MaxFP" + "SR2200" "mKateFP" "differences in adsorption or binding of stain" "far-red fluorescent protein tag" @@ -671,6 +680,7 @@ "Dronpa-3" "PA-CFP" "tissue in acrylic resin embedment" + "HiLyte647" "stiffness" "labeled primary antibody" "photoconvertible fluorescent protein" @@ -760,7 +770,8 @@ "FAIM" "fluorescence anisotropy imaging" "birefringence" - "FIB-SEM" + "focussed ion beam scanning electron microscopy" + "FIB-SEM" "inelastic scattering of photons" "Raman effect" "CARS microscopy" @@ -777,5 +788,6 @@ "cryo-scanning electron microscopy" "cryo-SEM" "FLIM" + "SBF-SEM" "polarized light microscopy" "anisotropy/polarization microscopy"