Galaxy |

Changeset 0:2c0c29a64e44 (2017-11-10)

Next changeset 1:a1836eeabc82 (2020-01-22)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6

added:
README.md
get_parent_terms_by_relationship_type.pl
get_relationship_id_vs_relationship_def.xml
get_terms_by_relationship_type.pl
onto_macros.xml
test-data/ancestors.tab
test-data/ancestors_rel_filtered.tab
test-data/children.tab
test-data/descendents.tab
test-data/lowest_common_ancestor.tab
test-data/parents.tab
test-data/pre_cco_core.obo
test-data/pre_cco_core.owl
test-data/relationship_id_vs_relationship_def.tab
test-data/relationship_id_vs_relationship_name.tab
test-data/relationship_id_vs_relationship_namespace.tab
test-data/relationship_types.tab
test-data/root_terms.tab
test-data/sub_ontology.obo
test-data/term_id_vs_term_def.tab
test-data/term_id_vs_term_name.tab
test-data/term_synonyms.tab
test-data/terms.tab
test-data/terms_rel_filtered.tab

diff -r 000000000000 -r 2c0c29a64e44 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,53 @@
+# README
+
+ONTO-Toolkit is a collection of Galaxy tools for managing ontologies
+that are represented in the OBO flat file format (spec 1.2 and 1.4).
+
+Those tools are basically wrappers around the most commonly used tools
+provided by the ONTO-PERL suite.
+
+See also:
+
+  1. ONTO-PERL: An API supporting the development and analysis of bio-ontologies
+     Antezana E, Egana M, De Baets B, Kuiper M, Mironov V.
+     Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
+
+  2. ONTO-Toolkit: A set of Galaxy tools to deal with OBO-formatted ontologies
+     Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M.
+     BMC Bioinformatics 2010, 11(Suppl 12):S8 doi:10.1186/1471-2105-11-S12-S8
+
+  3. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL.
+     Egana M, Fernandez-Breis JT, Antezana E.
+     Semantic Web Applications and Tools for Life Sciences (SWAT4LS), London, UK (2011)
+
+
+## CITING ONTO-Toolkit
+
+If you use ONTO-Toolkit in your work, you are kindly requested to cite:
+
+    ONTO-Toolkit: A set of Galaxy tools to deal with OBO-formatted ontologies
+    Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M.
+    BMC Bioinformatics 2010, 11(Suppl 12):S8 doi:10.1186/1471-2105-11-S12-S8
+
+
+## COPYRIGHT AND LICENCE
+
+Copyright (c) 2010-2014 Erick Antezana and Bjoern Gruening.
+OONTO-Toolkit is free software; you can redistribute it and/or
+modify it under the terms GPL3+, see the additional LICENSE file.
+
+
+
+## INSTALLATION
+
+It is recommended to install this wrapper via the `Galaxy Tool Shed`.
+
+.. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/bgruening/onto_perl_toolkit
+
+
+## History
+
+- v1.41.0: Initial release, forked from https://toolshed.g2.bx.psu.edu/view/erick-antezana/onto-toolkit
+with kind permission from Erick Antezana, who is the main developer of the underlying PERL library.
+
+

diff -r 000000000000 -r 2c0c29a64e44 get_parent_terms_by_relationship_type.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/get_parent_terms_by_relationship_type.pl Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,34 @@
+#!/usr/bin/perl
+
+eval 'exec /usr/bin/perl  -S $0 ${1+"$@"}'
+   if 0; # not running under some shell
+
+
+use Carp;
+use strict;
+use warnings;
+
+use OBO::Parser::OBOParser;
+
+my $my_parser = OBO::Parser::OBOParser->new();
+my $ontology  = $my_parser->work(shift(@ARGV));
+my $term_id   = shift(@ARGV);
+my $rel_id    = shift(@ARGV);
+
+my $target_term = $ontology->get_term_by_id($term_id);
+my @rels        = @{$ontology->get_relationships_by_source_term($target_term, $rel_id)};
+
+foreach my $r (@rels) {
+      # print "rel: ", $r->id(), "\n";
+       print $r->head()->id();
+      # print "tail: ", $r->tail()->id(), "\n\n";
+}
+
+exit 0;
+__END__
+
+
+
+
+
+

diff -r 000000000000 -r 2c0c29a64e44 get_relationship_id_vs_relationship_def.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/get_relationship_id_vs_relationship_def.xml Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,36 @@
+<tool id="onto_tk_get_relationship_id_vs_relationship_def" name="Get all the relationship IDs and definitions" version="@VERSION@.0">
+    <description>from the given OBO ontology</description>
+    <macros>
+        <import>onto_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive">
+    get_relationship_id_vs_relationship_def.pl
+        -f '$input' | sort > '$output'
+    </command>
+    <inputs>
+        <expand macro="input_ontology" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="Relationship IDs and definitions of ${on_string}">
+            <actions>
+                <action name="column_names" type="metadata" default="releationship ID,releationship definition" />
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="pre_cco_core.obo"/>
+            <output name="output" file="relationship_id_vs_relationship_def.tab"/>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+Generates a flat file with two columns (TAB separated) with the relationship_id and relationship_definition from the elements of the given OBO ontology.
+
+    </help>
+    <expand macro="citations" />
+</tool>
+

diff -r 000000000000 -r 2c0c29a64e44 get_terms_by_relationship_type.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/get_terms_by_relationship_type.pl Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,28 @@
+#!/usr/bin/perl
+
+eval 'exec /usr/bin/perl  -S $0 ${1+"$@"}'
+   if 0; # not running under some shell
+
+use Carp;
+use strict;
+use warnings;
+use Encode;
+
+use OBO::Parser::OBOParser;
+
+my $my_parser     = OBO::Parser::OBOParser->new();
+my $ontology      = $my_parser->work(shift(@ARGV));
+my $rel_type_name = shift(@ARGV);
+my @relationships = @{$ontology->get_relationships()};
+
+foreach my $r (@relationships) {
+ if($r->type() eq $rel_type_name){
+ print $r->tail()->id(), "\t";
+ print $r->type(),"\t";
+ print $r->head()->id(), "\n";
+ }
+}
+
+exit 0;
+
+__END__

diff -r 000000000000 -r 2c0c29a64e44 onto_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/onto_macros.xml Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,37 @@
+<macros>
+    <token name="@VERSION@">1.45</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">perl-onto-perl</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="input_ontology">
+        <param name="input" format="obo" type="data" label="Ontology file"/>
+    </xml>
+    <xml name="term_id">
+        <param name="term_id" type="text" value="" label="Term ID">
+            <expand macro="sanitize_ids" />
+        </param>
+    </xml>
+    <xml name="rel_id">
+        <param name="rel_id" type="text" value="" label="Relationship ID">
+            <expand macro="sanitize_ids" />
+        </param>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/1471-2105-11-S12-S8</citation>
+        </citations>
+    </xml>
+    <xml name="sanitize_ids">
+        <sanitizer invalid_char="">
+            <valid initial="string.letters,string.digits"><add value="_" /><add value=":" /> </valid>
+        </sanitizer>
+    </xml>
+    <xml name="sanitize_urls">
+        <sanitizer invalid_char="">
+            <valid initial="string.letters,string.digits"><add value="_" /><add value=":" /><add value="/" /></valid>
+        </sanitizer>
+    </xml>
+</macros>

diff -r 000000000000 -r 2c0c29a64e44 test-data/ancestors.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ancestors.tab Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,11 @@
+CCO:P0000016 M phase of mitotic cell cycle
+CCO:P0000019 mitotic anaphase
+CCO:P0000037 mitotic cell cycle
+CCO:P0000038 M phase
+CCO:P0000056 cell cycle
+CCO:P0000069 mitosis
+CCO:P0000266 anaphase
+CCO:P0000308 cell cycle process
+CCO:P0000309 cell cycle phase
+CCO:U0000000 cell-cycle entity
+CCO:U0000002 cell-cycle process

diff -r 000000000000 -r 2c0c29a64e44 test-data/ancestors_rel_filtered.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ancestors_rel_filtered.tab Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,1 @@
+CCO:P0000069
\ No newline at end of file

diff -r 000000000000 -r 2c0c29a64e44 test-data/children.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/children.tab Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,21 @@
+CCO:P0000031 mitotic prometaphase
+CCO:P0000032 leptotene
+CCO:P0000033 zygotene
+CCO:P0000034 pachytene
+CCO:P0000035 diplotene
+CCO:P0000036 diakinesis
+CCO:P0000038 M phase
+CCO:P0000069 mitosis
+CCO:P0000103 meiosis
+CCO:P0000104 meiosis I
+CCO:P0000112 meiosis II
+CCO:P0000118 male meiosis I
+CCO:P0000119 male meiosis II
+CCO:P0000262 G1 phase
+CCO:P0000263 G2 phase
+CCO:P0000264 S phase
+CCO:P0000266 anaphase
+CCO:P0000267 metaphase
+CCO:P0000268 prophase
+CCO:P0000269 interphase
+CCO:P0000270 telophase

diff -r 000000000000 -r 2c0c29a64e44 test-data/descendents.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/descendents.tab Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,2 @@
+CCO:P0000020 mitotic anaphase A
+CCO:P0000021 mitotic anaphase B

diff -r 000000000000 -r 2c0c29a64e44 test-data/lowest_common_ancestor.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lowest_common_ancestor.tab Fri Nov 10 11:34:06 2017 -0500

[

@@ -0,0 +1,9 @@
+
+ description: Get the lowest common ancestor (LCA) of two terms in a given OBO ontology.
+ usage      : get_lowest_common_ancestor.pl [options]
+ options    :
+ -f   OBO input file
+ -a term 1 ID
+ -b term 2 ID
+ example:
+ perl get_lowest_common_ancestor.pl -f go.obo -t GO:0000234 -t GO:0000111

diff -r 000000000000 -r 2c0c29a64e44 test-data/parents.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/parents.tab Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,2 @@
+CCO:P0000265 meiotic cell cycle
+CCO:P0000308 cell cycle process

diff -r 000000000000 -r 2c0c29a64e44 test-data/pre_cco_core.obo
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pre_cco_core.obo Fri Nov 10 11:34:06 2017 -0500

[

b'@@ -0,0 +1,3845 @@\n+format-version: 1.2\n+date: 16:02:2007 16:06\n+default-namespace: CCO\n+autogenerated-by: ONTO-PERL\n+remark: The Cell-Cycle Ontology\n+\n+[Term]\n+id: CCO:B0000000\n+name: core cell cycle protein\n+def: "A protein being considered as principal in the regulation of the cell cycle process" [CCO:cco_team]\n+is_a: CCO:U0000005 ! protein\n+\n+[Term]\n+id: CCO:P0000001\n+name: mitotic spindle elongation\n+def: "Lengthening of the distance between poles of the mitotic spindle." [GOC:mah]\n+is_a: CCO:P0000310 ! spindle elongation\n+relationship: part_of CCO:P0000058 ! mitotic spindle organization and biogenesis\n+synonym: "spindle elongation during mitosis" EXACT []\n+xref: GO:0000022\n+\n+[Term]\n+id: CCO:P0000002\n+name: mitotic sister chromatid segregation\n+def: "The cell cycle process whereby replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets." [GOC:ai]\n+is_a: CCO:P0000308 ! cell cycle process\n+relationship: part_of CCO:P0000069 ! mitosis\n+synonym: "mitotic chromosome segregation" EXACT []\n+synonym: "mitotic sister-chromatid adhesion release" NARROW []\n+xref: GO:0000070\n+xref: GO:0016359\n+\n+[Term]\n+id: CCO:P0000003\n+name: M phase specific microtubule process\n+def: "A microtubule-based process that occurs only during M phase of the cell cycle." [GOC:mah]\n+relationship: part_of CCO:P0000038 ! M phase\n+synonym: "M-phase specific microtubule process" EXACT []\n+xref: GO:0000072\n+\n+[Term]\n+id: CCO:P0000004\n+name: regulation of progression through cell cycle\n+def: "Any process that modulates the rate or extent of progression through the cell cycle." [GOC:go_curators]\n+is_a: CCO:P0000294 ! regulation of cell cycle\n+synonym: "cell cycle regulator" RELATED []\n+synonym: "RHEB small monomeric GTPase activity" RELATED []\n+synonym: "tumor suppressor" RELATED []\n+synonym: "control of cell cycle progression" EXACT []\n+synonym: "modulation of cell cycle progression" EXACT []\n+synonym: "regulation of cell cycle progression" EXACT []\n+xref: Reactome:156678\n+xref: Reactome:156699\n+xref: Reactome:156711\n+xref: Reactome:162657\n+xref: Reactome:165167\n+xref: Reactome:167104\n+xref: Reactome:167109\n+xref: Reactome:169311\n+xref: Reactome:171117\n+xref: Reactome:171122\n+xref: Reactome:174455\n+xref: Reactome:177752\n+xref: Reactome:177757\n+xref: GO:0000074\n+\n+[Term]\n+id: CCO:P0000005\n+name: cell cycle checkpoint\n+def: "A point in the eukaryotic cell cycle where progress through the cycle can be halted until conditions are suitable for the cell to proceed to the next stage." [GOC:mah, ISBN:0815316194]\n+is_a: CCO:P0000004 ! regulation of progression through cell cycle\n+xref: Reactome:69620\n+xref: GO:0000075\n+\n+[Term]\n+id: CCO:P0000006\n+name: DNA replication checkpoint\n+def: "A signal transduction based surveillance mechanism that prevents the initiation of mitosis until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome." [GOC:rn, PMID:11728327, PMID:12537518]\n+is_a: CCO:P0000157 ! DNA integrity checkpoint\n+xref: GO:0000076\n+\n+[Term]\n+id: CCO:P0000007\n+name: DNA damage checkpoint\n+def: "A signal transduction pathway, induced by DNA damage, that blocks cell cycle progression (in G1, G2 or metaphase) or slows the rate at which S phase proceeds." [PMID:11891124]\n+is_a: CCO:P0000157 ! DNA integrity checkpoint\n+synonym: "DNA damage response, signal transduction resulting in cell cycle arrest" NARROW []\n+xref: GO:0000077\n+\n+[Term]\n+id: CCO:P0000008\n+name: cell morphogenesis checkpoint\n+def: "A cell cycle checkpoint observed when aspects of polarity control are defective, which maintains coordination between the process of cellular morphogenesis and the nuclear events of the cell cycle. For example, in budding yeast cell-cycle dela'..b' earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.\n+is_a: relationship ! relationship\n+is_transitive: true\n+xref: OBO_REL:preceded_by\n+\n+[Typedef]\n+id: precedes\n+name: precedes\n+is_a: relationship ! relationship\n+is_transitive: true\n+xref: OBO_REL:precedes\n+\n+[Typedef]\n+id: proper_part_of\n+name: proper_part_of\n+def: "As for part_of, with the additional constraint that subject and object are distinct" [PMID:15892874]\n+is_a: part_of ! part_of\n+is_transitive: true\n+xref: OBO_REL:proper_part_of\n+\n+[Typedef]\n+id: relationship\n+name: relationship\n+def: "A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances." []\n+xref: OBO_REL:relationship\n+\n+[Typedef]\n+id: transformation_of\n+name: transformation_of\n+def: "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C\' if and only if given any c and any t, if c instantiates C at time t, then for some t\', c instantiates C\' at t\' and t\' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C\' at t2." [PMID:15892874]\n+comment: When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.\n+is_a: relationship ! relationship\n+is_transitive: true\n+xref: OBO_REL:transformation_of\n+\n+[Typedef]\n+id: transforms_into\n+name: transforms_into\n+is_a: relationship ! relationship\n+is_transitive: true\n+xref: CCO_REL:transforms_into\n+\n+[Typedef]\n+id: has_source\n+name: has_source\n+def: "o originates from O where o is a gene or gene product and O an organism." [CCO:ea]\n+is_a: relationship ! relationship\n+xref: CCO_REL:has_source\n+\n+[Typedef]\n+id: source_of\n+name: source_of\n+def: "O source of o where O is an organism and o a gene or gene product." [CCO:ea]\n+is_a: relationship ! relationship\n+xref: CCO_REL:source_of\n+\n+[Typedef]\n+id: has_function\n+name: has_function\n+is_a: relationship ! relationship\n+xref: OBO_REL:has_function\n'

diff -r 000000000000 -r 2c0c29a64e44 test-data/pre_cco_core.owl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pre_cco_core.owl Fri Nov 10 11:34:06 2017 -0500

b'@@ -0,0 +1,14035 @@\n+<?xml version="1.0"?>\n+<rdf:RDF\n+\txmlns="http://"\n+\txmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"\n+\txmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"\n+\txmlns:owl="http://www.w3.org/2002/07/owl#"\n+\txmlns:xsd="http://www.w3.org/2001/XMLSchema#"\n+\txmlns:oboInOwl="http://"\n+\txmlns:oboContent="http://"\n+\txml:base="http://CCO"\n+>\n+<owl:AnnotationProperty rdf:about="http://hasURI"/>\n+<owl:AnnotationProperty rdf:about="http://hasAlternativeId"/>\n+<owl:AnnotationProperty rdf:about="http://hasDate"/>\n+<owl:AnnotationProperty rdf:about="http://hasVersion"/>\n+<owl:AnnotationProperty rdf:about="http://hasDbXref"/>\n+<owl:AnnotationProperty rdf:about="http://hasDefaultNamespace"/>\n+<owl:AnnotationProperty rdf:about="http://hasNamespace"/>\n+<owl:AnnotationProperty rdf:about="http://hasDefinition"/>\n+<owl:AnnotationProperty rdf:about="http://hasExactSynonym"/>\n+<owl:AnnotationProperty rdf:about="http://hasNarrowSynonym"/>\n+<owl:AnnotationProperty rdf:about="http://hasBroadSynonym"/>\n+<owl:AnnotationProperty rdf:about="http://hasRelatedSynonym"/>\n+<owl:AnnotationProperty rdf:about="http://hasSynonymType"/>\n+<owl:AnnotationProperty rdf:about="http://hasSubset"/>\n+<owl:AnnotationProperty rdf:about="http://inSubset"/>\n+<owl:AnnotationProperty rdf:about="http://savedBy"/>\n+<owl:AnnotationProperty rdf:about="http://replacedBy"/>\n+<owl:AnnotationProperty rdf:about="http://consider"/>\n+<owl:Class rdf:about="http://DbXref"/>\n+<owl:Class rdf:about="http://Definition"/>\n+<owl:Class rdf:about="http://Subset"/>\n+<owl:Class rdf:about="http://Synonym"/>\n+<owl:Class rdf:about="http://SynonymType"/>\n+<owl:Class rdf:about="http://ObsoleteClass"/>\n+<owl:ObjectProperty rdf:about="http://ObsoleteProperty"/>\n+\n+<owl:Ontology rdf:about="">\n+\t<oboInOwl:hasDate>16:02:2007 16:06</oboInOwl:hasDate>\n+\t<oboInOwl:hasDefaultNamespace>CCO</oboInOwl:hasDefaultNamespace>\n+\t<rdfs:comment>The Cell-Cycle Ontology</rdfs:comment>\n+</owl:Ontology>\n+\n+<owl:Class rdf:about="http://CCO#CCO_B0000000">\n+\t<rdfs:label xml:lang="en">core cell cycle protein</rdfs:label>\n+\t<oboInOwl:hasDefinition>\n+\t\t<oboInOwl:Definition>\n+\t\t\t<rdfs:label xml:lang="en">A protein being considered as principal in the regulation of the cell cycle process</rdfs:label>\n+\t\t\t<oboInOwl:hasDbXref>\n+\t\t\t\t<oboInOwl:DbXref>\n+\t\t\t\t\t<rdfs:label>CCO:cco_team</rdfs:label>\n+\t\t\t\t\t<oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://CCO#CCO_cco_team</oboInOwl:hasURI>\n+\t\t\t\t</oboInOwl:DbXref>\n+\t\t\t</oboInOwl:hasDbXref>\n+\t\t</oboInOwl:Definition>\n+\t</oboInOwl:hasDefinition>\n+\t<rdfs:subClassOf rdf:resource="http://CCO#CCO_U0000005"/>\n+</owl:Class>\n+\n+<owl:Class rdf:about="http://CCO#CCO_P0000001">\n+\t<rdfs:label xml:lang="en">mitotic spindle elongation</rdfs:label>\n+\t<oboInOwl:hasDefinition>\n+\t\t<oboInOwl:Definition>\n+\t\t\t<rdfs:label xml:lang="en">Lengthening of the distance between poles of the mitotic spindle.</rdfs:label>\n+\t\t\t<oboInOwl:hasDbXref>\n+\t\t\t\t<oboInOwl:DbXref>\n+\t\t\t\t\t<rdfs:label>GOC:mah</rdfs:label>\n+\t\t\t\t\t<oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://GOC#GOC_mah</oboInOwl:hasURI>\n+\t\t\t\t</oboInOwl:DbXref>\n+\t\t\t</oboInOwl:hasDbXref>\n+\t\t</oboInOwl:Definition>\n+\t</oboInOwl:hasDefinition>\n+\t<oboInOwl:hasExactSynonym>\n+\t\t<oboInOwl:Synonym>\n+\t\t\t<rdfs:label xml:lang="en">spindle elongation during mitosis</rdfs:label>\n+\t\t</oboInOwl:Synonym>\n+\t</oboInOwl:hasExactSynonym>\n+\t<oboInOwl:hasDbXref>\n+\t\t<oboInOwl:DbXref>\n+\t\t\t<rdfs:label>GO:0000022</rdfs:label>\n+\t\t\t<oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://GO#GO_0000022</oboInOwl:hasURI>\n+\t\t</oboInOwl:DbXref>\n+\t</oboInOwl:hasDbXref>\n+\t<rdfs:subClassOf rdf:resource="http://CCO#CCO_P0000310"/>\n+\t<rdfs:subClassOf>\n+\t\t<owl:Restriction>\n+\t\t\t<owl:onProperty>\n+\t\t\t\t<owl:ObjectProperty rdf:about="http://CCO#part_of"/>\n+\t\t\t</owl:onProperty>\n+\t\t\t<owl:someValuesFrom rdf:resource="http://CCO#CCO_P0000058"/>\n+\t\t</owl:Restriction>\n+\t</rdfs:subClassOf>\n+</owl:Class>\n+\n+<owl:Class rdf:abo'..b'el>CCO:ea</rdfs:label>\n+\t\t\t\t\t<oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://CCO#CCO_ea</oboInOwl:hasURI>\n+\t\t\t\t</oboInOwl:DbXref>\n+\t\t\t</oboInOwl:hasDbXref>\n+\t\t</oboInOwl:Definition>\n+\t</oboInOwl:hasDefinition>\n+\t<rdfs:subPropertyOf rdf:resource="http://CCO#relationship"/>\n+\t<oboInOwl:hasDbXref>\n+\t\t<oboInOwl:DbXref>\n+\t\t\t<rdfs:label>CCO_REL:source_of</rdfs:label>\n+\t\t\t<oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://CCO_REL#CCO_REL_source_of</oboInOwl:hasURI>\n+\t\t</oboInOwl:DbXref>\n+\t</oboInOwl:hasDbXref>\n+</owl:ObjectProperty>\n+\n+<owl:ObjectProperty rdf:about="http://CCO#transformation_of">\n+\t<rdfs:label xml:lang="en">transformation_of</rdfs:label>\n+\t<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.</rdfs:comment>\n+\t<oboInOwl:hasDefinition>\n+\t\t<oboInOwl:Definition>\n+\t\t\t<rdfs:label xml:lang="en">Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally&#58&#59; C transformation_of C\' if and only if given any c and any t, if c instantiates C at time t, then for some t\', c instantiates C\' at t\' and t\' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C\' at t2.</rdfs:label>\n+\t\t\t<oboInOwl:hasDbXref>\n+\t\t\t\t<oboInOwl:DbXref>\n+\t\t\t\t\t<rdfs:label>PMID:15892874</rdfs:label>\n+\t\t\t\t\t<oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://PMID#PMID_15892874</oboInOwl:hasURI>\n+\t\t\t\t</oboInOwl:DbXref>\n+\t\t\t</oboInOwl:hasDbXref>\n+\t\t</oboInOwl:Definition>\n+\t</oboInOwl:hasDefinition>\n+\t<rdfs:subPropertyOf rdf:resource="http://CCO#relationship"/>\n+\t<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>\n+\t<oboInOwl:hasDbXref>\n+\t\t<oboInOwl:DbXref>\n+\t\t\t<rdfs:label>OBO_REL:transformation_of</rdfs:label>\n+\t\t\t<oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://OBO_REL#OBO_REL_transformation_of</oboInOwl:hasURI>\n+\t\t</oboInOwl:DbXref>\n+\t</oboInOwl:hasDbXref>\n+</owl:ObjectProperty>\n+\n+<owl:ObjectProperty rdf:about="http://CCO#transforms_into">\n+\t<rdfs:label xml:lang="en">transforms_into</rdfs:label>\n+\t<rdfs:subPropertyOf rdf:resource="http://CCO#relationship"/>\n+\t<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>\n+\t<oboInOwl:hasDbXref>\n+\t\t<oboInOwl:DbXref>\n+\t\t\t<rdfs:label>CCO_REL:transforms_into</rdfs:label>\n+\t\t\t<oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://CCO_REL#CCO_REL_transforms_into</oboInOwl:hasURI>\n+\t\t</oboInOwl:DbXref>\n+\t</oboInOwl:hasDbXref>\n+</owl:ObjectProperty>\n+\n+</rdf:RDF>\n+\n+\n\\ No newline at end of file\n'

diff -r 000000000000 -r 2c0c29a64e44 test-data/relationship_id_vs_relationship_def.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/relationship_id_vs_relationship_def.tab Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,23 @@
+adjacent_to C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity
+association C in association with C' produces C'' if and only if for all c belonging to C and c' belongin to C', exists a c'' (belonging to C'') which is the result of the reversible union between c and c'.
+catalyses C catalyses P if and only if for all c (catalyst) belonging to C, exists a p (belonging to P) which chemical reaction rate is increased by c.
+codes_for g encodes for p where g a Gene and p is a Protein.
+contained_in C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)
+degradates C is degradated (into NIL) if and only if for all c belonging to C, exists c', c'', ... (belonging to C', C'', ...) which are the result of any undesired breakdown of c with impairment or loss of its characteristic properties.
+derives_from Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
+encoded_by p is encoded by g where p is a Protein and g a Gene.
+has_agent As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
+has_participant P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
+has_source o originates from O where o is a gene or gene product and O an organism.
+improper_part_of As for part_of, with the additional constraint that subject and object may be identical
+integral_part_of C integral_part_of C' if and only if: C part_of C' AND C' has_part C
+interacts_with C interacts_with C' if and only if for all c belonging to C, exists a c' (belonging to C') which plays a role with c'.
+is_a For continuants: C is_a C' if and only if: given any c that instantiates C at a time t, c instantiates C' at t. For processes: P is_a P' if and only if: that given any p that instantiates P, then p instantiates P'.
+located_in C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
+participates_in C participates_in P if and only if: given any continuant c that instantiates C there is some process p, and some time t, such that: p has part c at t
+part_of For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
+preceded_by P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
+proper_part_of As for part_of, with the additional constraint that subject and object are distinct
+relationship A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances.
+source_of O source of o where O is an organism and o a gene or gene product.
+transformation_of Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.

diff -r 000000000000 -r 2c0c29a64e44 test-data/relationship_id_vs_relationship_name.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/relationship_id_vs_relationship_name.tab Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,34 @@
+adjacent_to adjacent_to
+agent_in agent_in
+association association
+catalyses catalyses
+codes_for codes_for
+contained_in contained_in
+contains contains
+degradates degradates
+derived_into derived_into
+derives_from derives_from
+encoded_by encoded_by
+has_agent has_agent
+has_function has_function
+has_improper_part has_improper_part
+has_integral_part has_integral_part
+has_part has_part
+has_participant has_participant
+has_proper_part has_proper_part
+has_source has_source
+improper_part_of improper_part_of
+integral_part_of integral_part_of
+interacts_with interacts_with
+is_a is_a
+located_in located_in
+location_of location_of
+participates_in participates_in
+part_of part_of
+preceded_by preceded_by
+precedes precedes
+proper_part_of proper_part_of
+relationship relationship
+source_of source_of
+transformation_of transformation_of
+transforms_into transforms_into

diff -r 000000000000 -r 2c0c29a64e44 test-data/relationship_types.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/relationship_types.tab Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,34 @@
+adjacent_to
+agent_in
+association
+catalyses
+codes_for
+contained_in
+contains
+degradates
+derived_into
+derives_from
+encoded_by
+has_agent
+has_function
+has_improper_part
+has_integral_part
+has_part
+has_participant
+has_proper_part
+has_source
+improper_part_of
+integral_part_of
+interacts_with
+is_a
+located_in
+location_of
+participates_in
+part_of
+preceded_by
+precedes
+proper_part_of
+relationship
+source_of
+transformation_of
+transforms_into

diff -r 000000000000 -r 2c0c29a64e44 test-data/root_terms.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/root_terms.tab Fri Nov 10 11:34:06 2017 -0500

@@ -0,0 +1,1 @@
+CCO:U0000000 cell-cycle entity

diff -r 000000000000 -r 2c0c29a64e44 test-data/sub_ontology.obo
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sub_ontology.obo Fri Nov 10 11:34:06 2017 -0500

[

@@ -0,0 +1,12 @@
+format-version: 1.4
+date: 04:11:2017 20:49
+auto-generated-by: ONTO-PERL 1.45
+default-namespace: CCO
+remark: The Cell-Cycle Ontology
+
+[Term]
+id: CCO:P0000003
+name: M phase specific microtubule process
+def: "A microtubule-based process that occurs only during M phase of the cell cycle." [GOC:mah]
+synonym: "M-phase specific microtubule process" EXACT []
+xref: GO:0000072

diff -r 000000000000 -r 2c0c29a64e44 test-data/term_id_vs_term_def.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/term_id_vs_term_def.tab Fri Nov 10 11:34:06 2017 -0500

b"@@ -0,0 +1,326 @@\n+CCO:B0000000\tA protein being considered as principal in the regulation of the cell cycle process\n+CCO:P0000001\tLengthening of the distance between poles of the mitotic spindle.\n+CCO:P0000002\tThe cell cycle process whereby replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.\n+CCO:P0000003\tA microtubule-based process that occurs only during M phase of the cell cycle.\n+CCO:P0000004\tAny process that modulates the rate or extent of progression through the cell cycle.\n+CCO:P0000005\tA point in the eukaryotic cell cycle where progress through the cycle can be halted until conditions are suitable for the cell to proceed to the next stage.\n+CCO:P0000006\tA signal transduction based surveillance mechanism that prevents the initiation of mitosis until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome.\n+CCO:P0000007\tA signal transduction pathway, induced by DNA damage, that blocks cell cycle progression (in G1, G2 or metaphase) or slows the rate at which S phase proceeds.\n+CCO:P0000008\tA cell cycle checkpoint observed when aspects of polarity control are defective, which maintains coordination between the process of cellular morphogenesis and the nuclear events of the cell cycle. For example, in budding yeast cell-cycle delay or arrest is induced when aspects of bud formation are defective.\n+CCO:P0000009\tAny process that modulates the frequency, rate or extent of CDK activity.\n+CCO:P0000010\tProgression through G1 phase, one of two 'gap' phases in the mitotic cell cycle; G1 is the interval between the completion of mitosis and the beginning of DNA synthesis.\n+CCO:P0000011\tProgression from G1 phase to S phase of the mitotic cell cycle.\n+CCO:P0000012\tAny process that regulates transcription such that the target genes are transcribed during the G1/S phase of the mitotic cell cycle.\n+CCO:P0000013\tProgression through S phase, the part of the mitotic cell cycle during which DNA synthesis takes place.\n+CCO:P0000014\tProgression through G2 phase, one of two 'gap' phases in the mitotic cell cycle; G2 is the interval between the completion of DNA synthesis and the beginning of mitosis.\n+CCO:P0000015\tProgression from G2 phase to M phase of the mitotic cell cycle.\n+CCO:P0000016\tProgression through M phase, the part of the mitotic cell cycle during which mitosis and cytokinesis take place.\n+CCO:P0000017\tProgression through prophase, the initial stage of mitosis in which the chromosomes are condensed but are not yet attached to a mitotic spindle.\n+CCO:P0000018\tProgression through metaphase, the stage of mitosis at which chromosomes are firmly attached to the mitotic spindle at its equator but have not yet segregated to opposite poles.\n+CCO:P0000019\tProgression through anaphase, the stage of mitosis during which the two sets of chromosomes separate and move away from each other.\n+CCO:P0000020\tProgression through anaphase A, the part of mitotic anaphase in which the kinetochore microtubules shorten as chromosomes move toward the spindle poles.\n+CCO:P0000021\tProgression through anaphase B, the part of mitotic anaphase in which the polar microtubules elongate and the two poles of the spindle move farther apart.\n+CCO:P0000022\tProgression through telophase, the last of the stages of mitosis; in the canonical cell cycle, telophase begins when the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts.\n+CCO:P0000023\tAny process that regulates transcription such that the target genes are transcribed during the G1 phase of the mitotic cell cycle.\n+CCO:P0000024\tA cell cycle process that regulates transcription such that the target genes are transcribed during the S phase of the "..b'al elements form a proteinaceous core between the two sister chromatids of each chromosome; the two axial elements then connect along their entire lengths by fine fibers known as transverse filaments, forming the lateral elements.\n+CCO:P0000306\tThe processes by which a contractile ring is maintained in a location and prevented from moving elsewhere.\n+CCO:P0000307\tThe process by which progression through the cell cycle is halted in a cell that has been committed to become a neuron that will reside in the forebrain.\n+CCO:P0000308\tA cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.\n+CCO:P0000309\tA cell cycle process composed of one of the morphological steps through which a cell progresses during successive cell replication or nuclear replication events.\n+CCO:P0000310\tThe cell cycle process whereby the distance is lengthened between poles of the spindle.\n+CCO:P0000311\tThe cell cycle process whereby spindle midzone is formed. The spindle midzone is the area in the center of the spindle where the spindle microtubules from opposite poles overlap.\n+CCO:P0000312\tThe cell cycle process whereby paired chromosomes are detached from each other. In budding yeast, this includes the cleavage of cohesin complexes along the chromosome arms, followed by the separation of the centromeric regions.\n+CCO:P0000313\tThe cell cycle process whereby genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during a normally chiasmate meiosis under the condition that chiasma have not occurred between a particular pair of homologs. Distributive segregation is a \\"backup\\" mechanism to ensure the segregation of homologs that have failed to cross over -- either as a consequence of mutation or not, as, for example, the 4th chromosome of Drosophila melanogaster (which never exchanges, presumably due to its small size) -- but nevertheless segregate normally.\n+CCO:P0000314\tAny process that modulates the frequency, rate or extent of the cell cycle process whereby the distance is lengthened between poles of the spindle.\n+CCO:P0000315\tAny process that modulates the frequency, rate or extent of the cell cycle process whereby the distance is lengthened between poles of the mitotic spindle.\n+CCO:U0000000\tA process or continuant.\n+CCO:U0000001\tEntities which endure, or continue to exist, through time while undergoing different sort of changes, including changes of place.\n+CCO:U0000002\tEntities that unfold themselves in successive temporal phases.\n+CCO:U0000003\tA polymer, such as a protein, nucleic acid, or transcript, ocurring in, or formed by, living systems.\n+CCO:U0000004\tA locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions.\n+CCO:U0000005\tOne or more polypeptides which may, or may not, be covalently bonded, and which assume a native secondary and tertiary structure.\n+CCO:U0000006\tAn RNA synthesized on a DNA or RNA template by an RNA polymerase.\n+CCO:U0000007\tCell cycle proteins are polymeric macromolecules composed of one or more long chains of amino acids linked by peptide bonds, usually coiled and folded into complex globular or fibrous structures.\n+CCO:U0000008\tCell cycle units of heredity which (except for polygenes) may be regarded as the controlling agents in the expression of single phenotypic characters and are usually segments of a chromosome at fixed positions relative to each other.\n+CCO:U0000010\tAny distinct chemical species in which two or more identical or nonidentical chemical species are associated.\n+CCO:U0000011\tA modified protein\n+CCO:U0000012\tA cell cycle protein which underwent any sort of modification (e.g. phosphorylation)\n+CCO:U0000030\tA protein which underwent any sort of modification (e.g. phosphorylation)\n'

diff -r 000000000000 -r 2c0c29a64e44 test-data/term_id_vs_term_name.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/term_id_vs_term_name.tab Fri Nov 10 11:34:06 2017 -0500

b'@@ -0,0 +1,391 @@\n+CCO:B0000000\tcore cell cycle protein\n+CCO:P0000001\tmitotic spindle elongation\n+CCO:P0000002\tmitotic sister chromatid segregation\n+CCO:P0000003\tM phase specific microtubule process\n+CCO:P0000004\tregulation of progression through cell cycle\n+CCO:P0000005\tcell cycle checkpoint\n+CCO:P0000006\tDNA replication checkpoint\n+CCO:P0000007\tDNA damage checkpoint\n+CCO:P0000008\tcell morphogenesis checkpoint\n+CCO:P0000009\tregulation of cyclin-dependent protein kinase activity\n+CCO:P0000010\tG1 phase of mitotic cell cycle\n+CCO:P0000011\tG1/S transition of mitotic cell cycle\n+CCO:P0000012\tG1/S-specific transcription in mitotic cell cycle\n+CCO:P0000013\tS phase of mitotic cell cycle\n+CCO:P0000014\tG2 phase of mitotic cell cycle\n+CCO:P0000015\tG2/M transition of mitotic cell cycle\n+CCO:P0000016\tM phase of mitotic cell cycle\n+CCO:P0000017\tmitotic prophase\n+CCO:P0000018\tmitotic metaphase\n+CCO:P0000019\tmitotic anaphase\n+CCO:P0000020\tmitotic anaphase A\n+CCO:P0000021\tmitotic anaphase B\n+CCO:P0000022\tmitotic telophase\n+CCO:P0000023\tG1-specific transcription in mitotic cell cycle\n+CCO:P0000024\tS-phase-specific transcription in mitotic cell cycle\n+CCO:P0000025\tG2-specific transcription in mitotic cell cycle\n+CCO:P0000026\tG2/M-specific transcription in mitotic cell cycle\n+CCO:P0000027\testablishment of mitotic spindle orientation\n+CCO:P0000028\tseptin checkpoint\n+CCO:P0000029\tmeiotic spindle organization and biogenesis\n+CCO:P0000030\tM/G1 transition of mitotic cell cycle\n+CCO:P0000031\tmitotic prometaphase\n+CCO:P0000032\tleptotene\n+CCO:P0000033\tzygotene\n+CCO:P0000034\tpachytene\n+CCO:P0000035\tdiplotene\n+CCO:P0000036\tdiakinesis\n+CCO:P0000037\tmitotic cell cycle\n+CCO:P0000038\tM phase\n+CCO:P0000039\tcytokinesis after mitosis\n+CCO:P0000040\tre-entry into mitotic cell cycle\n+CCO:P0000041\tre-entry into mitotic cell cycle after pheromone arrest\n+CCO:P0000042\tachiasmate meiosis I\n+CCO:P0000043\tmeiotic DNA double-strand break processing\n+CCO:P0000044\tmeiotic DNA recombinase assembly\n+CCO:P0000045\tmeiotic strand invasion\n+CCO:P0000046\tmeiotic joint molecule formation\n+CCO:P0000047\tmeiotic mismatch repair\n+CCO:P0000048\tmeiotic DNA repair synthesis\n+CCO:P0000049\tresolution of meiotic joint molecules as recombinants\n+CCO:P0000050\tmeiotic heteroduplex formation\n+CCO:P0000051\tmeiotic strand displacement\n+CCO:P0000052\tcell cycle arrest in response to pheromone\n+CCO:P0000053\tnegative regulation of exit from mitosis\n+CCO:P0000054\tmeiotic gene conversion\n+CCO:P0000055\tDNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest\n+CCO:P0000056\tcell cycle\n+CCO:P0000057\tcell cycle arrest\n+CCO:P0000058\tmitotic spindle organization and biogenesis\n+CCO:P0000059\tmale meiotic spindle assembly (sensu Metazoa)\n+CCO:P0000060\tmale meiosis I spindle assembly (sensu Metazoa)\n+CCO:P0000061\tmale meiosis II spindle assembly (sensu Metazoa)\n+CCO:P0000062\tfemale meiotic spindle assembly (sensu Metazoa)\n+CCO:P0000063\tfemale meiosis I spindle assembly (sensu Metazoa)\n+CCO:P0000064\tfemale meiosis II spindle assembly (sensu Metazoa)\n+CCO:P0000065\tmale meiosis chromosome segregation\n+CCO:P0000066\tmitotic sister chromatid cohesion\n+CCO:P0000067\tmale meiosis sister chromatid cohesion\n+CCO:P0000068\tfemale meiosis sister chromatid cohesion\n+CCO:P0000069\tmitosis\n+CCO:P0000070\tnegative regulation of transcription, mitotic\n+CCO:P0000071\tnegative regulation of transcription from RNA polymerase I promoter, mitotic\n+CCO:P0000072\tnegative regulation of transcription from RNA polymerase II promoter, mitotic\n+CCO:P0000073\tnegative regulation of transcription from RNA polymerase III promoter, mitotic\n+CCO:P0000074\tactivation of transcription on exit from mitosis\n+CCO:P0000075\tactivation of transcription on exit from mitosis, from RNA polymerase I promoter\n+CCO:P0000076\tactivation of transcription on exit from mitosis, from RNA polymerase II promoter\n+CCO:P0000077\tactivation of transcription on exit from mitosis, from RNA polymerase III promoter\n+CCO:P0000078\tmitotic chromoso'..b'nt of spindle microtubules to kinetochore during meiosis II\n+CCO:P0000292\tanaphase-promoting complex activation during meiotic cell cycle\n+CCO:P0000293\tmeiotic recombination checkpoint\n+CCO:P0000294\tregulation of cell cycle\n+CCO:P0000295\tcell cycle switching, meiotic to mitotic cell cycle\n+CCO:P0000296\tcell cycle switching, mitotic to meiotic cell cycle\n+CCO:P0000297\tgermline cell cycle switching, mitotic to meiotic cell cycle\n+CCO:P0000298\tmeiotic sister chromatid cohesion, centromeric\n+CCO:P0000299\tmeiotic sister chromatid arm separation\n+CCO:P0000300\tmeiotic sister chromatid centromere separation\n+CCO:P0000301\tmeiotic sister chromatid separation\n+CCO:P0000302\thomologous chromosome movement towards spindle pole during meiosis I\n+CCO:P0000303\tsister chromosome movement towards spindle pole during meiosis II\n+CCO:P0000304\tmeiotic sister chromatid cohesion, arms\n+CCO:P0000305\tlateral element assembly\n+CCO:P0000306\tmaintenance of contractile ring localization\n+CCO:P0000307\tcell cycle arrest of committed forebrain neuronal progenitor cell\n+CCO:P0000308\tcell cycle process\n+CCO:P0000309\tcell cycle phase\n+CCO:P0000310\tspindle elongation\n+CCO:P0000311\tspindle midzone assembly\n+CCO:P0000312\tchromosome separation\n+CCO:P0000313\tdistributive segregation\n+CCO:P0000314\tregulation of spindle elongation\n+CCO:P0000315\tregulation of mitotic spindle elongation\n+CCO:T0000001\tTetrapoda organism\n+CCO:T0000002\tAscomycota organism\n+CCO:T0000003\tTheria organism\n+CCO:T0000004\tHomo sapiens organism\n+CCO:T0000005\tCoelomata organism\n+CCO:T0000006\tEuteleostomi organism\n+CCO:T0000007\trosids organism\n+CCO:T0000008\tSchizosaccharomyces organism\n+CCO:T0000009\tStreptophyta organism\n+CCO:T0000010\tMagnoliophyta organism\n+CCO:T0000011\torganism\n+CCO:T0000012\tViridiplantae organism\n+CCO:T0000013\tSchizosaccharomycetales organism\n+CCO:T0000014\tSaccharomycetales organism\n+CCO:T0000015\teudicotyledons organism\n+CCO:T0000016\tSaccharomyces cerevisiae organism\n+CCO:T0000017\tSchizosaccharomyces pombe organism\n+CCO:T0000018\tEuphyllophyta organism\n+CCO:T0000019\tSaccharomyces organism\n+CCO:T0000020\tMetazoa organism\n+CCO:T0000021\tHomo/Pan/Gorilla group organism\n+CCO:T0000022\tBrassicales organism\n+CCO:T0000023\tEmbryophyta organism\n+CCO:T0000024\tSchizosaccharomycetes organism\n+CCO:T0000025\tFungi organism\n+CCO:T0000026\tTeleostomi organism\n+CCO:T0000027\tBrassicaceae organism\n+CCO:T0000028\tPrimates organism\n+CCO:T0000029\tHominoidea organism\n+CCO:T0000030\tTracheophyta organism\n+CCO:T0000031\tSpermatophyta organism\n+CCO:T0000032\tEukaryota organism\n+CCO:T0000033\tArabidopsis thaliana organism\n+CCO:T0000034\tSaccharomycetaceae organism\n+CCO:T0000035\tBilateria organism\n+CCO:T0000036\tVertebrata organism\n+CCO:T0000037\tcore eudicotyledons organism\n+CCO:T0000038\tSaccharomycotina organism\n+CCO:T0000039\tSaccharomycetes organism\n+CCO:T0000040\tcellular organisms organism\n+CCO:T0000041\tFungi/Metazoa group organism\n+CCO:T0000042\tAmniota organism\n+CCO:T0000043\tDeuterostomia organism\n+CCO:T0000044\tCraniata organism\n+CCO:T0000045\tChordata organism\n+CCO:T0000046\tCatarrhini organism\n+CCO:T0000047\tSimiiformes organism\n+CCO:T0000048\tEumetazoa organism\n+CCO:T0000049\tGnathostomata organism\n+CCO:T0000050\tSarcopterygii organism\n+CCO:T0000051\tStreptophytina organism\n+CCO:T0000052\tHomo organism\n+CCO:T0000053\tEuarchontoglires organism\n+CCO:T0000054\tSchizosaccharomycetaceae organism\n+CCO:T0000055\tMammalia organism\n+CCO:T0000056\tEutheria organism\n+CCO:T0000057\tArabidopsis organism\n+CCO:T0000058\tHominidae organism\n+CCO:T0000059\tHaplorrhini organism\n+CCO:T0000060\teurosids II organism\n+CCO:U0000000\tcell-cycle entity\n+CCO:U0000001\tcell-cycle continuant\n+CCO:U0000002\tcell-cycle process\n+CCO:U0000003\tbiopolymer\n+CCO:U0000004\tgene\n+CCO:U0000005\tprotein\n+CCO:U0000006\ttranscript\n+CCO:U0000007\tcell cycle protein\n+CCO:U0000008\tcell cycle gene\n+CCO:U0000009\tinteraction\n+CCO:U0000010\tcomplex\n+CCO:U0000011\tmodified protein\n+CCO:U0000012\tcell cycle modified protein\n+CCO:U0000030\tmodified protein\n+CCO:Y0000025\tphysical association\n'

diff -r 000000000000 -r 2c0c29a64e44 test-data/terms.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/terms.tab Fri Nov 10 11:34:06 2017 -0500

diff -r 000000000000 -r 2c0c29a64e44 test-data/terms_rel_filtered.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/terms_rel_filtered.tab Fri Nov 10 11:34:06 2017 -0500

b'@@ -0,0 +1,454 @@\n+adjacent_to\tis_a\trelationship\n+agent_in\tis_a\trelationship\n+association\tis_a\trelationship\n+catalyses\tis_a\trelationship\n+CCO:B0000000\tis_a\tCCO:U0000005\n+CCO:P0000001\tis_a\tCCO:P0000310\n+CCO:P0000002\tis_a\tCCO:P0000308\n+CCO:P0000004\tis_a\tCCO:P0000294\n+CCO:P0000005\tis_a\tCCO:P0000004\n+CCO:P0000006\tis_a\tCCO:P0000157\n+CCO:P0000007\tis_a\tCCO:P0000157\n+CCO:P0000008\tis_a\tCCO:P0000005\n+CCO:P0000009\tis_a\tCCO:P0000004\n+CCO:P0000010\tis_a\tCCO:P0000262\n+CCO:P0000011\tis_a\tCCO:P0000308\n+CCO:P0000012\tis_a\tCCO:P0000308\n+CCO:P0000013\tis_a\tCCO:P0000264\n+CCO:P0000014\tis_a\tCCO:P0000263\n+CCO:P0000015\tis_a\tCCO:P0000308\n+CCO:P0000016\tis_a\tCCO:P0000038\n+CCO:P0000017\tis_a\tCCO:P0000268\n+CCO:P0000018\tis_a\tCCO:P0000267\n+CCO:P0000019\tis_a\tCCO:P0000266\n+CCO:P0000020\tis_a\tCCO:P0000019\n+CCO:P0000021\tis_a\tCCO:P0000019\n+CCO:P0000022\tis_a\tCCO:P0000270\n+CCO:P0000023\tis_a\tCCO:P0000308\n+CCO:P0000024\tis_a\tCCO:P0000308\n+CCO:P0000025\tis_a\tCCO:P0000308\n+CCO:P0000026\tis_a\tCCO:P0000308\n+CCO:P0000027\tis_a\tCCO:P0000177\n+CCO:P0000028\tis_a\tCCO:P0000005\n+CCO:P0000029\tis_a\tCCO:P0000308\n+CCO:P0000030\tis_a\tCCO:P0000308\n+CCO:P0000031\tis_a\tCCO:P0000309\n+CCO:P0000032\tis_a\tCCO:P0000309\n+CCO:P0000033\tis_a\tCCO:P0000309\n+CCO:P0000034\tis_a\tCCO:P0000309\n+CCO:P0000035\tis_a\tCCO:P0000309\n+CCO:P0000036\tis_a\tCCO:P0000309\n+CCO:P0000037\tis_a\tCCO:P0000056\n+CCO:P0000038\tis_a\tCCO:P0000309\n+CCO:P0000039\tis_a\tCCO:P0000308\n+CCO:P0000040\tis_a\tCCO:P0000004\n+CCO:P0000041\tis_a\tCCO:P0000040\n+CCO:P0000042\tis_a\tCCO:P0000104\n+CCO:P0000043\tis_a\tCCO:P0000308\n+CCO:P0000044\tis_a\tCCO:P0000308\n+CCO:P0000045\tis_a\tCCO:P0000308\n+CCO:P0000046\tis_a\tCCO:P0000308\n+CCO:P0000047\tis_a\tCCO:P0000308\n+CCO:P0000048\tis_a\tCCO:P0000308\n+CCO:P0000049\tis_a\tCCO:P0000254\n+CCO:P0000050\tis_a\tCCO:P0000308\n+CCO:P0000051\tis_a\tCCO:P0000308\n+CCO:P0000052\tis_a\tCCO:P0000057\n+CCO:P0000053\tis_a\tCCO:P0000095\n+CCO:P0000054\tis_a\tCCO:P0000308\n+CCO:P0000055\tis_a\tCCO:P0000158\n+CCO:P0000056\tis_a\tCCO:U0000002\n+CCO:P0000057\tis_a\tCCO:P0000198\n+CCO:P0000058\tis_a\tCCO:P0000308\n+CCO:P0000059\tis_a\tCCO:P0000242\n+CCO:P0000060\tis_a\tCCO:P0000059\n+CCO:P0000061\tis_a\tCCO:P0000059\n+CCO:P0000062\tis_a\tCCO:P0000242\n+CCO:P0000063\tis_a\tCCO:P0000062\n+CCO:P0000064\tis_a\tCCO:P0000062\n+CCO:P0000065\tis_a\tCCO:P0000189\n+CCO:P0000065\tis_a\tCCO:P0000308\n+CCO:P0000066\tis_a\tCCO:P0000308\n+CCO:P0000067\tis_a\tCCO:P0000240\n+CCO:P0000068\tis_a\tCCO:P0000240\n+CCO:P0000069\tis_a\tCCO:P0000309\n+CCO:P0000070\tis_a\tCCO:P0000206\n+CCO:P0000071\tis_a\tCCO:P0000070\n+CCO:P0000071\tis_a\tCCO:P0000216\n+CCO:P0000072\tis_a\tCCO:P0000070\n+CCO:P0000072\tis_a\tCCO:P0000218\n+CCO:P0000073\tis_a\tCCO:P0000070\n+CCO:P0000073\tis_a\tCCO:P0000220\n+CCO:P0000074\tis_a\tCCO:P0000308\n+CCO:P0000075\tis_a\tCCO:P0000074\n+CCO:P0000076\tis_a\tCCO:P0000074\n+CCO:P0000077\tis_a\tCCO:P0000074\n+CCO:P0000078\tis_a\tCCO:P0000308\n+CCO:P0000079\tis_a\tCCO:P0000308\n+CCO:P0000080\tis_a\tCCO:P0000308\n+CCO:P0000081\tis_a\tCCO:P0000308\n+CCO:P0000082\tis_a\tCCO:P0000308\n+CCO:P0000083\tis_a\tCCO:P0000308\n+CCO:P0000084\tis_a\tCCO:P0000308\n+CCO:P0000085\tis_a\tCCO:P0000308\n+CCO:P0000086\tis_a\tCCO:P0000308\n+CCO:P0000087\tis_a\tCCO:P0000004\n+CCO:P0000088\tis_a\tCCO:P0000124\n+CCO:P0000089\tis_a\tCCO:P0000308\n+CCO:P0000090\tis_a\tCCO:P0000308\n+CCO:P0000091\tis_a\tCCO:P0000282\n+CCO:P0000092\tis_a\tCCO:P0000005\n+CCO:P0000092\tis_a\tCCO:P0000087\n+CCO:P0000093\tis_a\tCCO:P0000092\n+CCO:P0000093\tis_a\tCCO:P0000164\n+CCO:P0000094\tis_a\tCCO:P0000092\n+CCO:P0000094\tis_a\tCCO:P0000159\n+CCO:P0000095\tis_a\tCCO:P0000087\n+CCO:P0000096\tis_a\tCCO:P0000308\n+CCO:P0000097\tis_a\tCCO:P0000308\n+CCO:P0000098\tis_a\tCCO:P0000252\n+CCO:P0000099\tis_a\tCCO:P0000096\n+CCO:P0000100\tis_a\tCCO:P0000179\n+CCO:P0000101\tis_a\tCCO:P0000179\n+CCO:P0000102\tis_a\tCCO:P0000056\n+CCO:P0000103\tis_a\tCCO:P0000309\n+CCO:P0000104\tis_a\tCCO:P0000309\n+CCO:P0000105\tis_a\tCCO:P0000268\n+CCO:P0000106\tis_a\tCCO:P0000308\n+CCO:P0000107\tis_a\tCCO:P0000308\n+CCO:P0000108\tis_a\tCCO:P0000308\n+CCO:P0000109\tis_a\tCCO:P0000267\n+CCO:P0000110\tis_a\tCCO:P0000266\n+CCO:P0000111\tis_a\tCCO:P0000270\n+CCO:P0000112\tis_a\tCCO:P0000309\n+CCO:P0000113\tis_a\tCCO:P0000268\n+CCO:P0000114\tis_a\tCCO'..b'0000293\tis_a\tCCO:P0000005\n+CCO:P0000293\tis_a\tCCO:P0000200\n+CCO:P0000294\tis_a\tCCO:P0000308\n+CCO:P0000295\tis_a\tCCO:P0000294\n+CCO:P0000296\tis_a\tCCO:P0000294\n+CCO:P0000297\tis_a\tCCO:P0000296\n+CCO:P0000298\tis_a\tCCO:P0000308\n+CCO:P0000299\tis_a\tCCO:P0000308\n+CCO:P0000300\tis_a\tCCO:P0000308\n+CCO:P0000301\tis_a\tCCO:P0000254\n+CCO:P0000302\tis_a\tCCO:P0000134\n+CCO:P0000303\tis_a\tCCO:P0000134\n+CCO:P0000304\tis_a\tCCO:P0000308\n+CCO:P0000305\tis_a\tCCO:P0000308\n+CCO:P0000307\tis_a\tCCO:P0000057\n+CCO:P0000309\tis_a\tCCO:P0000308\n+CCO:P0000310\tis_a\tCCO:P0000308\n+CCO:P0000311\tis_a\tCCO:P0000308\n+CCO:P0000312\tis_a\tCCO:P0000308\n+CCO:P0000313\tis_a\tCCO:P0000189\n+CCO:P0000315\tis_a\tCCO:P0000314\n+CCO:T0000001\tis_a\tCCO:T0000050\n+CCO:T0000002\tis_a\tCCO:T0000025\n+CCO:T0000003\tis_a\tCCO:T0000055\n+CCO:T0000004\tis_a\tCCO:T0000052\n+CCO:T0000005\tis_a\tCCO:T0000035\n+CCO:T0000006\tis_a\tCCO:T0000026\n+CCO:T0000007\tis_a\tCCO:T0000037\n+CCO:T0000008\tis_a\tCCO:T0000054\n+CCO:T0000009\tis_a\tCCO:T0000012\n+CCO:T0000010\tis_a\tCCO:T0000031\n+CCO:T0000011\tis_a\tCCO:U0000001\n+CCO:T0000012\tis_a\tCCO:T0000032\n+CCO:T0000013\tis_a\tCCO:T0000024\n+CCO:T0000014\tis_a\tCCO:T0000039\n+CCO:T0000015\tis_a\tCCO:T0000010\n+CCO:T0000016\tis_a\tCCO:T0000019\n+CCO:T0000017\tis_a\tCCO:T0000008\n+CCO:T0000018\tis_a\tCCO:T0000030\n+CCO:T0000019\tis_a\tCCO:T0000034\n+CCO:T0000020\tis_a\tCCO:T0000041\n+CCO:T0000021\tis_a\tCCO:T0000058\n+CCO:T0000022\tis_a\tCCO:T0000060\n+CCO:T0000023\tis_a\tCCO:T0000051\n+CCO:T0000024\tis_a\tCCO:T0000002\n+CCO:T0000025\tis_a\tCCO:T0000041\n+CCO:T0000026\tis_a\tCCO:T0000049\n+CCO:T0000027\tis_a\tCCO:T0000022\n+CCO:T0000028\tis_a\tCCO:T0000053\n+CCO:T0000029\tis_a\tCCO:T0000046\n+CCO:T0000030\tis_a\tCCO:T0000023\n+CCO:T0000031\tis_a\tCCO:T0000018\n+CCO:T0000032\tis_a\tCCO:T0000040\n+CCO:T0000033\tis_a\tCCO:T0000057\n+CCO:T0000034\tis_a\tCCO:T0000014\n+CCO:T0000035\tis_a\tCCO:T0000048\n+CCO:T0000036\tis_a\tCCO:T0000044\n+CCO:T0000037\tis_a\tCCO:T0000015\n+CCO:T0000038\tis_a\tCCO:T0000002\n+CCO:T0000039\tis_a\tCCO:T0000038\n+CCO:T0000040\tis_a\tCCO:T0000011\n+CCO:T0000041\tis_a\tCCO:T0000032\n+CCO:T0000042\tis_a\tCCO:T0000001\n+CCO:T0000043\tis_a\tCCO:T0000005\n+CCO:T0000044\tis_a\tCCO:T0000045\n+CCO:T0000045\tis_a\tCCO:T0000043\n+CCO:T0000046\tis_a\tCCO:T0000047\n+CCO:T0000047\tis_a\tCCO:T0000059\n+CCO:T0000048\tis_a\tCCO:T0000020\n+CCO:T0000049\tis_a\tCCO:T0000036\n+CCO:T0000050\tis_a\tCCO:T0000006\n+CCO:T0000051\tis_a\tCCO:T0000009\n+CCO:T0000052\tis_a\tCCO:T0000021\n+CCO:T0000053\tis_a\tCCO:T0000056\n+CCO:T0000054\tis_a\tCCO:T0000013\n+CCO:T0000055\tis_a\tCCO:T0000042\n+CCO:T0000056\tis_a\tCCO:T0000003\n+CCO:T0000057\tis_a\tCCO:T0000027\n+CCO:T0000058\tis_a\tCCO:T0000029\n+CCO:T0000059\tis_a\tCCO:T0000028\n+CCO:T0000060\tis_a\tCCO:T0000007\n+CCO:U0000001\tis_a\tCCO:U0000000\n+CCO:U0000002\tis_a\tCCO:U0000000\n+CCO:U0000003\tis_a\tCCO:U0000001\n+CCO:U0000004\tis_a\tCCO:U0000003\n+CCO:U0000005\tis_a\tCCO:U0000003\n+CCO:U0000006\tis_a\tCCO:U0000003\n+CCO:U0000007\tis_a\tCCO:U0000001\n+CCO:U0000007\tis_a\tCCO:U0000005\n+CCO:U0000008\tis_a\tCCO:U0000001\n+CCO:U0000008\tis_a\tCCO:U0000004\n+CCO:U0000009\tis_a\tCCO:U0000002\n+CCO:U0000010\tis_a\tCCO:U0000001\n+CCO:U0000011\tis_a\tCCO:U0000005\n+CCO:U0000012\tis_a\tCCO:U0000007\n+CCO:U0000012\tis_a\tCCO:U0000011\n+CCO:U0000030\tis_a\tCCO:U0000005\n+CCO:Y0000025\tis_a\tCCO:U0000009\n+codes_for\tis_a\trelationship\n+contained_in\tis_a\trelationship\n+contains\tis_a\trelationship\n+degradates\tis_a\trelationship\n+derived_into\tis_a\trelationship\n+derives_from\tis_a\trelationship\n+encoded_by\tis_a\trelationship\n+has_agent\tis_a\trelationship\n+has_function\tis_a\trelationship\n+has_improper_part\tis_a\tpart_of\n+has_integral_part\tis_a\tpart_of\n+has_participant\tis_a\trelationship\n+has_part\tis_a\trelationship\n+has_proper_part\tis_a\tpart_of\n+has_source\tis_a\trelationship\n+improper_part_of\tis_a\tpart_of\n+integral_part_of\tis_a\tpart_of\n+interacts_with\tis_a\trelationship\n+located_in\tis_a\trelationship\n+location_of\tis_a\trelationship\n+participates_in\tis_a\trelationship\n+part_of\tis_a\trelationship\n+preceded_by\tis_a\trelationship\n+precedes\tis_a\trelationship\n+proper_part_of\tis_a\tpart_of\n+source_of\tis_a\trelationship\n+transformation_of\tis_a\trelationship\n+transforms_into\tis_a\trelationship\n'