diff --git a/docs/examples/imports-nucleus.owl b/docs/examples/imports-nucleus.owl new file mode 100644 index 000000000..0b4cc87ff --- /dev/null +++ b/docs/examples/imports-nucleus.owl @@ -0,0 +1,22 @@ +@prefix : . +@prefix owl: . +@prefix rdf: . +@prefix xml: . +@prefix xsd: . +@prefix rdfs: . +@base . + + rdf:type owl:Ontology ; + owl:imports . + +################################################################# +# Classes +################################################################# + +### http://purl.obolibrary.org/obo/GO_0005739 + rdf:type owl:Class ; + rdfs:subClassOf ; + rdfs:label "mitochondrion" . + + +### Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi diff --git a/docs/examples/mitochondrion-full.owl b/docs/examples/mitochondrion-full.owl new file mode 100644 index 000000000..5acf4e0ff --- /dev/null +++ b/docs/examples/mitochondrion-full.owl @@ -0,0 +1,666 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BFO:0000050 + external + part_of + part_of + part of + + + + + + + + + BFO:0000051 + external + has_part + has_part + has part + + + + + + + + + + + + + A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). + GO:0008372 + NIF_Subcellular:sao-1337158144 + NIF_Subcellular:sao1337158144 + cell or subcellular entity + cellular component + cellular_component + subcellular entity + GO:0005575 + + + + + + + + + Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + cellular_component + + + + + A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). + GOC:pdt + NIF_Subcellular:sao-1337158144 + + + + + subcellular entity + NIF_Subcellular:nlx_subcell_100315 + + + + + + + + + The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. + Wikipedia:Intracellular + internal to cell + protoplasm + cellular_component + nucleocytoplasm + protoplast + GO:0005622 + + + + + + intracellular + + + + + The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. + ISBN:0198506732 + + + + + nucleocytoplasm + GOC:mah + + + + + protoplast + GOC:mah + + + + + + + + + The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. + cell and encapsulating structures + NIF_Subcellular:sao1813327414 + Wikipedia:Cell_(biology) + cellular_component + GO:0005623 + + + + cell + + + + + The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. + GOC:go_curators + + + + + + + + + All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + MIPS_funcat:70.03 + Wikipedia:Cytoplasm + cellular_component + GO:0005737 + + + + + + + + cytoplasm + + + + + All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + ISBN:0198547684 + + + + + + + + + + A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. + MIPS_funcat:70.16 + NIF_Subcellular:sao1860313010 + Wikipedia:Mitochondrion + mitochondria + cellular_component + GO:0005739 + + + + + + + + + + + Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) + mitochondrion + + + + + A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. + GOC:giardia + ISBN:0198506732 + + + + + + + + + Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. + NIF_Subcellular:sao1539965131 + Wikipedia:Organelle + cellular_component + GO:0043226 + + + + organelle + + + + + Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + NIF_Subcellular:sao414196390 + membrane-enclosed organelle + cellular_component + GO:0043227 + membrane-bounded organelle + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + cellular_component + GO:0043229 + + intracellular organelle + + + + + Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + intracellular membrane-enclosed organelle + cellular_component + GO:0043231 + + intracellular membrane-bounded organelle + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. + cellular_component + GO:0044422 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + organelle part + + + + + Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. + cellular_component + GO:0044424 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + intracellular part + + + + + Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. + NIF_Subcellular:sao666410040 + mitochondrial subcomponent + mitochondrion component + cellular_component + GO:0044429 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + mitochondrial part + + + + + Any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. + GOC:jl + + + + + mitochondrial subcomponent + NIF_Subcellular:sao666410040 + + + + + + + + + + + + + + + + + + + + + + + + + + Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + cytoplasm component + cellular_component + GO:0044444 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + cytoplasmic part + + + + + Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + GOC:jl + + + + + + + + + + + + + + + + A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. + cellular_component + GO:0044446 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + intracellular organelle part + + + + + A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + Any constituent part of a cell, the basic structural and functional unit of all organisms. + NIF_Subcellular:sao628508602 + cellular subcomponent + cellular_component + protoplast + GO:0044464 + + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + cell part + + + + + Any constituent part of a cell, the basic structural and functional unit of all organisms. + GOC:jl + + + + + cellular subcomponent + NIF_Subcellular:sao628508602 + + + + + protoplast + GOC:mah + + + + + + + + + + + + + + + + + + + + + Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm" + cellular_component + GO:0099568 + cytoplasmic region + + + + + Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm" + GOC:dos + + + + + + + diff --git a/docs/examples/mitochondrion.owl b/docs/examples/mitochondrion.owl new file mode 100644 index 000000000..d6258d259 --- /dev/null +++ b/docs/examples/mitochondrion.owl @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + mitochondrion + + + + + + + + + + + + + diff --git a/docs/extract.md b/docs/extract.md index 81197e588..7a4c0c986 100644 --- a/docs/extract.md +++ b/docs/extract.md @@ -9,8 +9,6 @@ The reuse of ontology terms creates links between data, making the ontology and See `uberon_module.txt` for an example of a term file. Terms should be listed line by line, and comments can be included with `#`. Individual terms can be specified with `--term` followed by the CURIE. -NOTE: The `extract` command works on the input ontology, not its imports. To extract from imports you should first [merge](/merge). - The `--method` options fall into two groups: Syntactic Locality Module Extractor (SLME) and Minimum Information to Reference an External Ontology Term (MIREOT). - STAR: use the SLME to extract a fixpoint-nested module @@ -18,7 +16,25 @@ The `--method` options fall into two groups: Syntactic Locality Module Extractor - BOT: use the SLME to extract a bottom module - MIREOT: extract a simple hierarchy of terms -By default, `extract` will include imported ontologies. To exclude imported ontologies, just add `--imports exclude` for any non-MIREOT extraction method. +## Imports + +By default, `extract` will include imported ontologies. To exclude imported ontologies, just add `--imports exclude` for any non-MIREOT extraction method: + + robot extract --method BOT \ + --input imports-nucleus.owl \ + --term GO:0005739 \ + --imports exclude \ + --output mitochondrion.owl + +This only includes what is asserted in `imports-nucleus.owl`, which imports `nucleus.owl`. `imports-nucleus.owl` only includes the term 'mitochondrion' (`GO:0005739`) and links it to its parent class, 'intracellular membrane-bounded organelle' (`GO:0043231`). `nucleus.owl` contains the full hierarchy down to 'intracellular membrane-bounded organelle'. The output module, `mitochondrion.owl`, only includes the term 'mitochondrion' and this subClassOf statement. + +By contrast, including imports returns the full hierarchy down to 'mitochondrion', which is asserted in `nucleus.owl`: + + robot extract --method BOT \ + --input imports-nucleus.owl \ + --term GO:0005739 \ + --imports include \ + --output mitochondrion-full.owl ## Syntactic Locality Module Extractor (SLME)