diff --git a/src/ontology/OntoFox_inputs/GAZ_input.txt b/src/ontology/OntoFox_inputs/GAZ_input.txt new file mode 100644 index 00000000..2803a97e --- /dev/null +++ b/src/ontology/OntoFox_inputs/GAZ_input.txt @@ -0,0 +1,21 @@ +[URI of the OWL(RDF/XML) output file] +http://purl.obolibrary.org/obo/obi/dev/import/GAZ_imports.owl + +[Source ontology] +# Gazetteer +GAZ + +[Low level source term URIs] +http://purl.obolibrary.org/obo/GAZ_00000448 # geographic location + +[Top level source term URIs and target direct superclass URIs] +http://purl.obolibrary.org/obo/GAZ_00000448 # geographic location +subClassOf http://purl.obolibrary.org/obo/BFO_0000029 # site + +[Source term retrieval setting] +includeNoIntermediates + +[Source annotation URIs] +http://www.w3.org/2000/01/rdf-schema#label +copyTo http://purl.obolibrary.org/obo/IAO_0000111 +http://purl.obolibrary.org/obo/IAO_0000115 diff --git a/src/ontology/OntoFox_inputs/IAO_input.txt b/src/ontology/OntoFox_inputs/IAO_input.txt new file mode 100644 index 00000000..6ed4e251 --- /dev/null +++ b/src/ontology/OntoFox_inputs/IAO_input.txt @@ -0,0 +1,77 @@ +[URI of the OWL(RDF/XML) output file] +http://purl.obolibrary.org/obo/obi/dev/import/IAO_imports.owl + +[Source ontology] +# Information Artifact Ontology +IAO + +[Low level source term URIs] +http://purl.obolibrary.org/obo/IAO_0000001 # conditional specification +http://purl.obolibrary.org/obo/IAO_0000003 # measurement unit label +http://purl.obolibrary.org/obo/IAO_0000004 # has measurement value +http://purl.obolibrary.org/obo/IAO_0000005 # objective specification +http://purl.obolibrary.org/obo/IAO_0000006 # narrative object +http://purl.obolibrary.org/obo/IAO_0000009 # datum label +http://purl.obolibrary.org/obo/IAO_0000010 # software +http://purl.obolibrary.org/obo/IAO_0000027 # data item +http://purl.obolibrary.org/obo/IAO_0000028 # symbol +http://purl.obolibrary.org/obo/IAO_0000030 # information content entity +http://purl.obolibrary.org/obo/IAO_0000032 # scalar measurement datum +http://purl.obolibrary.org/obo/IAO_0000033 # directive information entity +http://purl.obolibrary.org/obo/IAO_0000037 # dot plot +http://purl.obolibrary.org/obo/IAO_0000038 # graph +http://purl.obolibrary.org/obo/IAO_0000039 # has measurement unit label +http://purl.obolibrary.org/obo/IAO_0000055 # rule +http://purl.obolibrary.org/obo/IAO_0000064 # algorithm +http://purl.obolibrary.org/obo/IAO_0000078 # curation status specification +http://purl.obolibrary.org/obo/IAO_0000079 # density plot +http://purl.obolibrary.org/obo/IAO_0000088 # report +http://purl.obolibrary.org/obo/IAO_0000098 # data format specification +http://purl.obolibrary.org/obo/IAO_0000100 # data set +http://purl.obolibrary.org/obo/IAO_0000101 # image +http://purl.obolibrary.org/obo/IAO_0000104 # plan specification +http://purl.obolibrary.org/obo/IAO_0000109 # measurement datum +http://purl.obolibrary.org/obo/IAO_0000136 # is about +http://purl.obolibrary.org/obo/IAO_0000144 # conclusion textual entity +http://purl.obolibrary.org/obo/IAO_0000178 # material information bearer +http://purl.obolibrary.org/obo/IAO_0000179 # histogram +http://purl.obolibrary.org/obo/IAO_0000180 # heatmap +http://purl.obolibrary.org/obo/IAO_0000183 # dendrogram +http://purl.obolibrary.org/obo/IAO_0000184 # scatter plot +http://purl.obolibrary.org/obo/IAO_0000219 # denotes +http://purl.obolibrary.org/obo/IAO_0000221 # is quality measurement of +http://purl.obolibrary.org/obo/IAO_0000300 # textual entity +http://purl.obolibrary.org/obo/IAO_0000306 # table +http://purl.obolibrary.org/obo/IAO_0000310 # document +http://purl.obolibrary.org/obo/IAO_0000312 # publication about an investigation +http://purl.obolibrary.org/obo/IAO_0000401 # one dimensional cartesian spatial coordinate datum +http://purl.obolibrary.org/obo/IAO_0000407 # has coordinate unit label +http://purl.obolibrary.org/obo/IAO_0000408 # length measurement datum +http://purl.obolibrary.org/obo/IAO_0000413 # is duration of +http://purl.obolibrary.org/obo/IAO_0000414 # mass measurement datum +http://purl.obolibrary.org/obo/IAO_0000416 # time measurement datum +http://purl.obolibrary.org/obo/IAO_0000422 # postal address +http://purl.obolibrary.org/obo/IAO_0000429 # email address +http://purl.obolibrary.org/obo/IAO_0000572 # documenting +http://purl.obolibrary.org/obo/IAO_0000573 # line graph +http://purl.obolibrary.org/obo/IAO_0000574 # assigning a centrally registered identifier +http://purl.obolibrary.org/obo/IAO_0000577 # centrally registered identifier symbol +http://purl.obolibrary.org/obo/IAO_0000594 # software application + +[Top level source term URIs and target direct superclass URIs] +http://purl.obolibrary.org/obo/IAO_0000030 # information content entity +subClassOf http://purl.obolibrary.org/obo/BFO_0000031 # generically dependent continuant +http://purl.obolibrary.org/obo/IAO_0000178 # material information bearer +subClassOf http://purl.obolibrary.org/obo/BFO_0000040 # material entity +http://purl.obolibrary.org/obo/IAO_0000574 # assigning a centrally registered identifier +subClassOf http://purl.obolibrary.org/obo/OBI_0000011 # planned process +http://purl.obolibrary.org/obo/IAO_0000572 # documenting +subClassOf http://purl.obolibrary.org/obo/OBI_0000011 # planned process + +[Source term retrieval setting] +includeAllIntermediates + +[Source annotation URIs] +http://www.w3.org/2000/01/rdf-schema#label +copyTo http://purl.obolibrary.org/obo/IAO_0000111 +http://purl.obolibrary.org/obo/IAO_0000115 diff --git a/src/ontology/OntoFox_inputs/PATO_input.txt b/src/ontology/OntoFox_inputs/PATO_input.txt index 4103876c..bb23fc9b 100755 --- a/src/ontology/OntoFox_inputs/PATO_input.txt +++ b/src/ontology/OntoFox_inputs/PATO_input.txt @@ -8,6 +8,8 @@ PATO http://purl.obolibrary.org/obo/PATO_0000011 http://purl.obolibrary.org/obo/PATO_0000018 http://purl.obolibrary.org/obo/PATO_0000047 +http://purl.obolibrary.org/obo/PATO_0000122 # length +http://purl.obolibrary.org/obo/PATO_0000125 # mass http://purl.obolibrary.org/obo/PATO_0000146 http://purl.obolibrary.org/obo/PATO_0000186 http://purl.obolibrary.org/obo/PATO_0000383 diff --git a/src/ontology/OntoFox_outputs/GAZ_imports.owl b/src/ontology/OntoFox_outputs/GAZ_imports.owl new file mode 100644 index 00000000..27c9f22b --- /dev/null +++ b/src/ontology/OntoFox_outputs/GAZ_imports.owl @@ -0,0 +1,118 @@ + + + + + + + + + + + + + + + editor preferred term~editor preferred label + editor preferred term~editor preferred label + + + + + + + + definition + definition + + + + + + + + imported from + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + geographic location + A reference to a place on the Earth, by its name or by its geographical location. + + geographic location + + + + + + + diff --git a/src/ontology/OntoFox_outputs/IAO_imports.owl b/src/ontology/OntoFox_outputs/IAO_imports.owl new file mode 100644 index 00000000..6515eb96 --- /dev/null +++ b/src/ontology/OntoFox_outputs/IAO_imports.owl @@ -0,0 +1,807 @@ + + + + + + + + + + + + + + + editor preferred term + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + editor preferred term + + + + + + + + definition + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + definition + + + + + + + + imported from + + + + + + + + + + + + + + + + + + + + has part + a core relation that holds between a whole and its part + + has part + + + + + + + + + + has measurement unit label + + has measurement unit label + + + + + + + + is about + A (currently) primitive relation that relates an information artifact to an entity. + + is about + + + + + + + + + denotes + A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically + + denotes + + + + + + + + + is quality measurement of + m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q + + is quality measurement of + + + + + + + + + + has coordinate unit label + + has coordinate unit label + + + + + + + + + is duration of + relates a process to a time-measurement-datum that represents the duration of the process + + is duration of + + + + + + + + + + + + + + has measurement value + + has measurement value + + + + + + + + + + + + + + + + + + + + + + + + + + conditional specification + A directive information entity that specifies what should happen if the trigger condition is fulfilled. + + conditional specification + + + + + + + + + measurement unit label + A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. + + measurement unit label + + + + + + + + + objective specification + A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. + + objective specification + + + + + + + + + narrative object + A narrative object is an information content entity that is a set of propositions. + + narrative object + + + + + + + + + datum label + A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label + + datum label + + + + + + + + + software + Software is a plan specification composed of a series of instructions that can be +interpreted by or directly executed by a processing unit. + + software + + + + + + + + + data item + 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. + + data item + + + + + + + + + symbol + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + + symbol + + + + + + + + + information content entity + A generically dependent continuant that is about some thing. + + information content entity + + + + + + + + + scalar measurement datum + A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. + + scalar measurement datum + + + + + + + + + directive information entity + An information content entity whose concretizations indicate to their bearer how to realize them in a process. + + directive information entity + + + + + + + + + dot plot + A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. + + dot plot + + + + + + + + + graph + A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. + + graph + + + + + + + + + rule + A rule is an executable which guides, defines, restricts actions. + + rule + + + + + + + + + algorithm + A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. + + algorithm + + + + + + + + + curation status specification + 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. + + curation status specification + + + + + + + + + density plot + A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. + + density plot + + + + + + + + + report + A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). + + report + + + + + + + + + data format specification + A data format specification is the information content borne by the document published defining the specification. +Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file + + data format specification + + + + + + + + + data set + A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. + + data set + + + + + + + + + image + An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. + + image + + + + + + + + + data about an ontology part + Data about an ontology part is a data item about a part of an ontology, for example a term + + data about an ontology part + + + + + + + + + plan specification + A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. + + plan specification + + + + + + + + + measurement datum + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + + measurement datum + + + + + + + + + conclusion textual entity + A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. + + conclusion textual entity + + + + + + + + + material information bearer + A material entity in which a concretization of an information content entity inheres. + + material information bearer + + + + + + + + + histogram + A histogram is a report graph which is a statistical description of a +distribution in terms of occurrence frequencies of different event classes. + + histogram + + + + + + + + + heatmap + A heatmap is a report graph which is a graphical representation of data +where the values taken by a variable(s) are shown as colors in a +two-dimensional map. + + heatmap + + + + + + + + + dendrogram + A dendrogram is a report graph which is a tree diagram +frequently used to illustrate the arrangement of the clusters produced by a +clustering algorithm. + + dendrogram + + + + + + + + + scatter plot + A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. + + scatter plot + + + + + + + + + textual entity + A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. + + textual entity + + + + + + + + + table + A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions + + table + + + + + + + + + figure + An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. + + figure + + + + + + + + + diagram + A figure that expresses one or more propositions + + diagram + + + + + + + + + document + A collection of information content entities intended to be understood together as a whole + + document + + + + + + + + + publication + A document that is the output of a publishing process. + + publication + + + + + + + + + publication about an investigation + A publication that is about an investigation + + publication about an investigation + + + + + + + + + cartesian spatial coordinate datum + A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude + + cartesian spatial coordinate datum + + + + + + + + + one dimensional cartesian spatial coordinate datum + A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region + + one dimensional cartesian spatial coordinate datum + + + + + + + + + length measurement datum + A scalar measurement datum that is the result of measurement of length quality + + length measurement datum + + + + + + + + + mass measurement datum + A scalar measurement datum that is the result of measurement of mass quality + + mass measurement datum + + + + + + + + + time measurement datum + A scalar measurement datum that is the result of measuring a temporal interval + + time measurement datum + + + + + + + + + postal address + A textual entity that is used as directive to deliver something to a person, or organization + + postal address + + + + + + + + + email address + + email address + + + + + + + + + documenting + A planned process in which a document is created or added to by including the specified input in it. + + documenting + + + + + + + + + line graph + A line graph is a type of graph created by connecting a series of data +points together with a line. + + line graph + + + + + + + + + assigning a centrally registered identifier + A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity + + assigning a centrally registered identifier + + + + + + + + + centrally registered identifier symbol + A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. + + centrally registered identifier symbol + + + + + + + + + software application + A software application is software that can be directly executed by some processing unit. + + software application + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/OntoFox_outputs/PATO_imports.owl b/src/ontology/OntoFox_outputs/PATO_imports.owl index d9a353c7..c29b780f 100644 --- a/src/ontology/OntoFox_outputs/PATO_imports.owl +++ b/src/ontology/OntoFox_outputs/PATO_imports.owl @@ -62,37 +62,9 @@ - - - - continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - - continuant - - - - - - - quality - - quality - - - - - - - - - specifically dependent continuant - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - - specifically dependent continuant - + @@ -159,7 +131,6 @@ - morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. @@ -181,6 +152,30 @@ + + + + + length + A 1-D extent quality which is equal to the distance between two points. + + length + + + + + + + + + mass + A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. + + mass + + + + @@ -397,18 +392,6 @@ - - - - - electromagnetic (EM) radiation quality - A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. - - electromagnetic (EM) radiation quality - - - - @@ -424,7 +407,7 @@ - + optical quality An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. @@ -664,7 +647,7 @@ - + cellular quality A monadic quality of continuant that exists at the cellular level of organisation. @@ -757,26 +740,26 @@ - + - + - 3-D extent - A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. + 1-D extent + A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. - 3-D extent + 1-D extent - + - - - radiation quality - A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. + + + 3-D extent + A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. - radiation quality + 3-D extent @@ -784,7 +767,7 @@ - + activity (of a radionuclide) A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate. @@ -994,6 +977,30 @@ fluid flow rate + + + + + + + + anatomical structure quality + A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. + + anatomical structure quality + + + + + + + + + quality of interaction of a substance with electromagnetic radiation + A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength. + + quality of interaction of a substance with electromagnetic radiation + diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 11d0ae46..37551192 100755 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -7,8 +7,10 @@ + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 6b4e0064..34a754c0 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -14,16 +14,18 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + - + + @@ -3196,6 +3198,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + planned process Injecting mice with a vaccine in order to test its efficacy @@ -3653,6 +3656,7 @@ objectives is a planned process. + @@ -22315,30 +22319,26 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - + + + + 0 + + + primary cultured cell population Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. 2013-6-5 MHB: This OBI class was formerly called 'primary cell culture', but label changed and definition updated following CLO alignment work. Previous definition: 'a primary cell culture is a cell culture where the cells derive from a fresh tissue source.' + consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. PERSON:Matthew Brush primary cell culture primary cell culture sample PERSON:Matthew Brush primary cultured cell population - - - 0 - - - - - - - consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. - @@ -27582,6 +27582,7 @@ Manual editing of automatically recorded data in an anesthesia information manag +