blipkit

load_ext.pro
bioprolog_util.pro
aggregate_by/4	DEPRECATED - use swi-prolog aggregate/4 instead.
atom_to_tokens/2	as atom_to_tokens/3, uses default_token_list/1.
atom_to_tokens/3	converts an atom into a list of token atoms.
call_det/1	calls Goal once, throws exception if Goal does not succeed.
call_on_stream/3	Goal should include StreamTemplate example: call_on_stream(S,sgml_write(S,Node,[]),XML).
codes_to_tokens/2
codes_to_tokens/3	converts a list of tokens into a list of token atoms optional tokenlist (as codes); defaults to 9,10,13,32.
compare_two_lists/4	List1 and List2 must be sorted in advance.
count_by/3	partition all distinct solutions to Goal into a list of groups, each group is a compound term of the form Template-Count.
count_by/4	partition all distinct solutions to Goal into a list of groups, each group is a compound term of the form Template-Count.
dsetof/3	deterministic setof.
ensure_nonvar/2	If Var is ground, do nothing.
findmax/4	as findmax/5.
findmax/5	of all instantiations Template gets on backtracking over Goal, find the best, where the best is defined by Val (which must be in Template) Example: =|findmax(Label,Len,(entity_label(E,Label),atom_length(Label,Len)),T,V).
forall_strict/2	all builtin predicate forall/2, throws an error if Action fails for any Cond.
getopt/2	FileL unifies with list of files after processing command line options.
group_by/3	partition all distinct solutions to Goal into a list of groups, each group is a compound term of the form Template-[Goal1, ...] Example: group_by(Job,person_job(_,Job),JobToTermList).
group_by/4	partition all distinct solutions to Goal into a list of groups, each group is a compound term of the form Template-[GroupingElement1, ...] Example: group_by(Job,person_job(Person,Job),Person,JobToTermList).
iterate_over_input/3	as iterate_over_input/3, uses current_input/1.
iterate_over_input/4	reads input from InStream, writing Prompt and transforming input.
list_avg/2	average value of all elements in list.
list_max/2	finds maximum value in list according to arithmetic function max DEPRECATED: use max_list/2 in library(lists).
list_min/2	finds minimum value in list according to arithmetic function min DEPRECATED: use min_list/2 in library(lists).
list_to_tuple/2	see also tuple_to_list/1 .
load_factfile/1	consults a prolog fact file.
load_factfile/2	as load_factfile/1, but explicitly load into module Mod.
load_factfiles/1	as load_factfile/1 but loads a list of fact files.
number_setof/3
oneof/1	calls Goal once.
pred_to_unground_term/2	translates a predicate specification into an unground term e.g.
read_file_to_tokens/2
setof_count/3	number of distinct solutions.
solutions/3	deterministic setof (will not fail).
sumof/3	Sum is unified with the aggregate sum of all Templates satisfying Goal.
term_gensym/3	generates or fetches a unique ID for Term in namespace NS uses get_time/1 to ensure uniqueness.
time_goal/2	calls Goal and unifies Time with the cputime taken.
tuple_to_list/2	converts tuples of form (X,Y) to list.
write_termrow/1	writes a predicate out as a tab delimited line, with predicate name as first column uses writecols/1.
write_termrow/2	as write_termrow/1 but to a stream.
writecols/1	write each element in a list separated by tabs.
writecols/2	write each element in a list separated by an atom code.
dbmeta.pro
datapred/2	this is a dynamic db fact, specifying that Pred is defined in Mod.
db_fact/2	nd.
db_facts/2	db_facts(+Mod,?Ts) is det.
fact_clausesource/2	true if Fact was defined in File.
insert_fact_with_source/2	as insert_fact/1, in addition records the source (eg filename).
insert_facts/2	adds facts to the prolog database.
leftjoin/2	relational left join between X and Y i.e.
materialize_view/2	materialize a view (intensional predicate).
materialize_views/1	generates facts for all extensional predicates in DbModule TEST.
merge_facts/2
pred_query/3	TEST.
write_db_fact_chain/2	as write_db_fact_chain/3.
write_db_fact_chain/3	Fact is a term corresponding to a term in a database.
write_db_summary/1	writes all facts in all db modules in database.
write_db_summary/2
graph.pro
closure/3
closure_contains_cycle/1	true if the closure of Rel commencing from NodeIDorIDs contains a cycle.
closure_contains_cycle/2	true if the closure of Rel commencing from NodeIDorIDs contains a cycle.
closure_dist/4
closure_path/4
closure_to_edgelist/3
closure_to_edgelist_delta/4
closure_to_edgelist_delta/5
edgelist_to_trees/2	given a list of edges between nodes in the graph, return a denormalized tree rooted at the sources.
inverse/3
inverse/4
minimal_spanning_node/3	as spanning_node/3, but only computes the minimal set - i.e.
reflexive_closure/3	The reflexive closure of a relation includes the reflexive relation.
spanning_node/3
graphviz.pro
display_graph/2	displays a graph using Cmd.
graph_to_dot/2	converts a graph representation to a dot string.
graph_to_file/3	writes a graph to an img file using 'dot'.
index_util.pro
materialize_goal_to_file/2
materialize_goals_to_file/2
materialize_index/1	materialize and index a set of facts, using first-argument indexing.
materialize_indexes_to_file/2	if File does not exist, materializes a set of indexes and caches results in File.
io.pro
add_to_include_list/2	All IDs of this type will be include in export.
consult_bioconf/0	reads in a user's bioconf.pro file.
consult_bioconf/1	consult a particular bioconf.pro file.
file_to_prolog_cmd/2	maps file formats (obo, sbml, etc) to an executable that will parse the file to prolog facts.
format_module/2	maps file formats (obo, sbml, etc) to bio modules (ontol_db, sb_db).
load_biofile/1	loads a file - format is guessed from suffix.
load_biofile/2	loads a file - you have to specify the full path.
load_biofiles/1	loads a list of files - format is guessed from suffix.
load_bioresource/1	% load_bioresources(+ResList).
unload_biofile/2	removes all facts defined in File from the database.
unload_bioresource/1	only works with dynamic data - see unload_biofile/2.
write_biofile/1	see load_biofile/2.
load_blipcore.pro
macros_transitive.pro
mode.pro
mode/1	mode declaration; eg :- mode foo(X,Y) is det when (var(X),nonvar(Y)).
parser_general.pro
pp.pro
peval/1	use meta-circular interpreter to perform or-parallel evaluation of Goal.
peval/2	perform a pass-through execution of Goal.
safe_interpreter.pro
simmatrix.pro
attribute_feature_count/2	number of features that have attribute A.
attribute_information_content/2	-log2(p(A)) note: you may wish to memoize this using the blipkit tabling module.
attribute_pair_pval_hyper/3	calculates correlation between two attributes based on shared features.
compare_feature_pair/4	Opts : metric(Metric) - one of simj, cossim, ci, or a list of Metrics.
feature_matches/2	what does F match?
feature_matches/3	what does F match?
feature_pair_avgICCS/3
feature_pair_avgICCS/4	for each direct attribute, find the best match(es) in the other set.
feature_pair_ci/3	intersection of attribute values: | attrs(F1) ��� attrs(F2) |.
feature_pair_cossim/3	cosine similarity between two feature attributes vectors.
feature_pair_cu/3	union of attribute values: | attrs(F1) ��� attrs(F2) |.
feature_pair_maxIC/3	Max[IC(a)] : a ��� A1 ��� A2.
feature_pair_maxIC_attributes/4	Max[IC(a)] : a ��� A1 ��� A2.
feature_pair_nr_ICatt_pairs/4
feature_pair_simGIC/3	��� [a ��� A1 ��� A2] IC(a) / ��� [a ��� A1 ��� A2]IC(t) Ref: Pesquita, C.;Faria, D.;Bastos, H.;Falc��o, AO.; Couto, FM.
feature_pair_simj/3	Jacard similarity coefficient between two features, based on their attribute vectors: | A1 ��� A2| / | A1 ��� A2| where A1 and A2 are the sets of positive attributes in F1 and F2 respectively.
feature_pair_subset_of/3	degree to which F1 is a subset of F2.
feature_vector/2	relationship between a Feature and a vector of binary attribute values, encoded as a large int (the GMP library is required).
generate_term_indexes/3	creates an initial index of all features and attributes, using Goal to specify the feature to attribute relation.
vector_attributes/2	True if AV is an integer bit vector with the attributes in AL set.
suffixtree.pro
is_stree/1	succeeds if ST is a suffix tree.
stree_has/2	Tests if a string is a substring of some word inserted into the suffix tree % stree_has(?SymList,+ST) Generate string is a substring of some word inserted into the suffix tree.
stree_insert/3	Inserts a word into a suffix tree.
stree_insert_list/3	Insert a list of words into a suffix tree.
tabling.pro
clear_table_pred/1
persistent_table_pred/2	as table_pred/1, with persistence of the results of called predicates.
table_call/5	you should not need to call this directly.
table_pred/1
table_preds/0	call table_pred/1 for all predicates for which memoize_hook/1 is defined.
curation_bridge_to_ontol.pro
curation_bridge_to_ontol_core.pro
curation_bridge_to_ontol_reif.pro
curation_db.pro
class_coannotated_with/2
class_conditional_prob/3	ProbAGivenB = p(A|B) A and B are classes.
class_conditional_prob/5	ProbAGivenB = p(A|B) A and B are classes.
class_infocontent/2	IC = -log2(p(Class)).
class_prob/2
curation/1	true if Curation denotes a curated statement.
curation_evidence/2
curation_publisher/2	combination of curation/1 and entity_publisher/2 in GO annotation, the publisher is the source/assigned_by column.
curation_qualifier/3	col 4 in GAF.
curation_source/2	combination of curation/1 and entity_source/2 provenance of curation - eg PubMed identifier.
curation_statement/3	as curation_statement/4.
curation_statement/4	each curation can have zero to many statements (a curation is typically a single statement).
curation_statement/4	as curation_statement/4, but exclude redundant annotations (redundancy checked via parentT/2).
curation_statementT/4	as curation_statementT/5.
curation_statementT/5	true if Subject is annotated to ObDirect, and Ob is in the reflexive transitive closure of ObDirect; i.e.
curation_statement_evidence_type/4
curation_statement_evidence_type/5
curation_subject_property_value/4	col16 in GAF.
evidence_type/2
evidence_with/2
featureset_class_enrichment/2	FSampleMembers - each member must match a feature/1 tabling recommended - curation_statementT/4 and parentT/2.
negative_curation_statement/4
curation_writer_obo.pro
load_curation.pro
bioseq.pro
index_all_seqs_to_file/2	det word-index all bioseq/3 facts and write index to file F.
revcomp/2	reverse-complements a DNA sequence, represented as an atom.
sub_sequence/3	if Len<0 or End<Beg, the extracted sequence will be reverse complemented using revcomp/2.
translate_dna/2	as translate_dna/3, uses default eukaryotic genetic code (1).
translate_dna/3	translates a dna sequence (represented as an atom) to an amino acid sequence.
fasta_db.pro
fastaseq/3
gencode.pro
codon_aa/3
gencode_organism/2
genome_db.pro
exon_gene/2	composition of exon_transcript_order/3 .
gene_left_of/2	true if the genomic extent of G1 is < G2 .
gene_length/2	length of gene on genome.
gene_overlaps/2	true if the genomic extent of G1 and G2 share at least one base.
gene_polypeptide/2	TODO: mixing pp and cds for now....
genome_sqlmap_enscore.pro
gff.pro
codons_from_cds.pro
exon_transcript.pro
gruleset_enscore.pro
intron.pro
single_exon_gene.pro
hmm.pro
most_probable_hmm_path/2	true if Path is a list of the most probable output types for each token in Word.
iupac.pro
load_genomic.pro
parser_fasta.pro
range.pro
intersects/2	succeeds if Range1 and Range2 intersect [ignores strand] if Ranges are relative to a sequence, checks to make sure sequence is the same.
point_overlaps/2
project_point/3	coordinate transformation.
range_beg/2
range_end/2
range_max/2
range_min/2
range_orientation/2
relative_range/3	coordinate transformation.
reverse_project_point/3	reverse of project_point/3 TODO: can we use clp to make this more elegant?
seqanalysis_db.pro
hit/5	Example: hit('BLASTN-na1-na2.fa -na2', 'BLASTN-na1-na2.fa ', na2, na2, 'cp-of-na1-w-50bp-missing').
hit_acc/2	shorthand for hit/5.
hit_result/2	links hit with parent result see hit/5.
hsp/14	Example: hsp('BLASTN-na1-na2.fa -na2-2', 'BLASTN-na1-na2.fa -na2', 100.0, 12, 0, 0, 75, 87, 0, 85, 73, 0, 0.011, 24.3).
hsp_cigar/2	Example: hsp_cigar('BLASTN-na1-na2.fa -na2-0', '261M') .
hsp_hit/2	shorthand for hsp/14.
parse_cigar/2	parses a compact CIGAR atom into a list of transition states.
project_point_over_hsp/3	given an interbase position, project this from a query sequence to a hit sequence.
result/4	The result of running an analysis program over a query sequence, typically against a sequence database Example: a blast result.
result_param/3	tag-value parameters.
result_program/2	links results with program name See result/2.
result_statistic/3	tag-value statistics.
seqfeature_db.pro
concat_subfeature_residues/3	unifies Seq with an atom containing residues of all subfeatures of a certain type concatenated together.
coord_on_processed_transcript/4	maps integer coords between genome and processed transcript mode: nondet (via different exons??? TODO fix this?).
coord_on_processed_transcript/4
feature/1	TODO: fix Type to use identifier, not label/name.
feature/3
feature_by_type_id/3	nd.
feature_by_typename/3	nd.
feature_cvterm/2	as feature_cvterm/3, untyped.
feature_cvterm/3
feature_dbxref/2
feature_dbxref/3	DEPRECATED.
feature_end_junction/2
feature_label/2
feature_organism/2
feature_range/2	finds the range of a feature - always a single interval (i.e.
feature_rangeset/2	finds the range of a feature; the range term can be used with the range module.
feature_relationship/2	as feature_relationship/3, untyped.
feature_relationship/4
feature_residues/2
feature_seqlen/2
feature_start_junction/2
feature_type/2	TODO: fix Type to use identifier, not label/name.
featureloc/5
featureloc/8
featureprop/3
featureset_intersects/2	tests if two features intersect.
featureset_intersects/2	tests if two features intersect.
implied_feature_type/2
implied_feature_type/3
map_coordsystem/2	Range = gff(S,E,D) | interbase(Min,Max,Dir) | directional_interbase(B,E,Dir).
pp_from_start_codon/3	infers polypeptide seq and range (outermost extent) given a stop codon feature ID.
range_on_processed_transcript/4	maps a location from genome coords to processed transcript coords mode: nondet (via different exons TODO fix this?).
seqfeature_owlmap_node_as_class.pro
seqfeature_owlmap_node_as_class_basic.pro
seqfeature_owlmap_node_as_individual.pro
seqfeature_sqlmap_chado.pro
seqfeature_sqlmap_chado_exposed_ids.pro
seqfeature_sqlmap_go.pro
seqfeature_writer_chaos.pro
seqfeature_xmlmap_chado.pro
seqfeature_xmlmap_chaos.pro
seqfeature_xmlmap_game.pro
dotwriter.pro
graph_display/2	displays a graph using Cmd.
graph_display/3	displays a graph in Fmt using Cmd.
graph_nest/3	given a graph term and a set of edge labels, translate the graph such that edges of the designated type are translated to subgraphs (clusters in graphviz).
graph_nest_pairs/3	use NestPairs to nest the graph.
graph_to_dot_atom/2	translate a graph to an atom in dot syntax.
graph_to_dot_file/2	translate Graph to dot and write to File.
graph_to_dot_file/3
metadata_db.pro
current_time_iso_full/1	returns UTC time in ISO 8601 e.g.
entity_alternate_identifier/2	both Entity and AltID denote the same entity same as alt_id.
entity_comment/2	true if Comment is a human-readable text comment associated with Entity.
entity_created/2	true if Entity created on Date Date is in form YYYY-MM-DD.
entity_created_by/2
entity_creation_date/2	Date must conform to ISO-8601.
entity_label/2	it is recommended (required?) that entities have a single label use entity_synonym/2 for multiple labels.
entity_obsolete/2	true if Entity is a retired identifier, and Predicate(Entity) was once true.
entity_partition/2	true if Entity belongs to Partition.
entity_resource/2	true if Entity is derived from Source - Source denotes a logical source, for example an identifier for a publication.
entity_resource/2	true if Entity comes from Resource, where Resource is a physical resource - typically a file, URI or namespace not to be confused with entity_source/2 - the distinction is logical vs physical.
id_idspace/2	true if ID is prefixed with IDSpace.
id_localid/2	true if ID is suffixed with IDSpace.
idspace/1
idspace_uri/2	maps IDspaces (aka namespaces) such as GO to URI prefixes -- such as http://purl.org/obo/owl/GO#.
many_to_one_xref/3
one_to_many_xref_list/3	all xrefs for E in idspace S, where |set of xrefs| > 1.
partition/1	true if Partition identifies a subset of entities grouped together for some purpose.
same_label_as/2	true if X and Y share the same label or synonym.
metadata_nlp.pro
add_synonyms_minus_words/1	used to generate a version of an ontology for a particular context.
entity_label_token/2	see entity_label_token/3.
entity_label_token/3	each entity has multiple labels, and each label has multiple tokens.
entity_label_token_stemmed/4
entity_nlabel_scope_stemmed/4	performs normalization on labels * dehyphenate/2 * uses synset/1 (which also uses obol relational adjectives) * canonical token ordering * removes all whitespaces note that relational adjectives will not work in stemmed mode.
entity_pair_label_best_match/3	true if A and B share labels, and there is no B' such that B' is a better match for A, where better match is defined in terms of synonym scope (exact syns or labels beat other syns).
entity_pair_label_reciprocal_best_intermatch/3	as entity_pair_label_best_intermatch/3, (i.e.
entity_pair_label_reciprocal_best_match/3	as entity_pair_label_best_match/3, but only holds if base relation holds in both directions.
entity_pair_label_reciprocal_best_match/3	as entity_pair_label_best_match/3, but A and B must be in different ID spaces.
entity_pair_nlp_subset_of/3	ensure index_labels/1 is called first.
label_query_results/3	MaxScorePairsDesc = [Score1-Entity1, ...].
simindex_corpus_by_labels/4	e.g.
term_entity_matches/2
term_split/6	e.g term_split(x:foo_bar,x:foo,x:bar,exact,exact,exact).
term_split_over/7	true if E = A W B.
term_tokenset_stemmed/3	translates a term such as 'foo bar two hippocampi' to a set such as [2,bar,foo,hippocamp].
load_ontol.pro
ontol_bridge_from_owl.pro
ontol_bridge_from_owl2.pro
owlrestriction_to_oborelationship/2
ontol_bridge_to_owl.pro
ontol_bridge_to_owl2.pro
uri_oboid/2
ontol_db.pro
all_some/1	DEPRECATED: see below - but used in ontol_reasoner :- extensional(all_some/1).
belongs/2	true if Entity belongs to Ontology - equivalent to entity_resource/2 may be deprecated in future - consider entity_resource/2.
bf_parentRT/2	true if PID is reachable from ID via parent/2.
bf_set_parentRT/2	as bf_parentRT/2, starting point is a list.
cardinality_restriction/4	A relationship between two classes such that all instances of ?Class stand in ?Relation to ?Card instance(s) of ?ToClass.
cdef_label/2	generates a label from a cdef.
cdef_placement/5
class/1	class declaration - true if Class is a class.
class/2	combines class/1 and entity_label/2.
class_cdef/2	true if CDef is asserted to be equivalent to C (e.g.
class_comment/2	Combines class/1 and entity_comment/2 holds when class(Class) and entity_comment(Class,Comment).
class_disjoint_union_list/2	inferred from disjoint_from/2 and class_union_element/2.
class_instrule/3	Class(HeadVars) :- Body is a rule for instantiating Class.
class_intersection_element/2	for definitions.
class_label/3	true if Class has name or synonym Label (case-insensitive) Label='exact' for names and exact synonyms; otherwise synonym type see class/2 and synonym/3.
class_level_inverse_of/2	DEPRECATED: just use inverse_of true if Inverse is the inverse of Relation, such that the inverse is held between classes formally: restriction(X,R,Y),class_inverse(R,R1) => restriction(Y,R1,X).
class_pair_subclass_lca/3	true if LCA is a common ancestor of X and Y by subclassRT/2, and if there exists no other more recent CA.
class_reified_rulebody/3	reified form of class_instrule/3.
class_union_element/2	for covering axioms.
class_xref/2
complement_of/2	EXPERIMENTAL.
cyclic_form_of/2
cyclic_over/2
def/2	true if DefinitionText is the natural language definition of Class or Relation % def(+Class,?DefinitionText) is semidet.
def_xref/2	true if DBXRef is the source of the def/2 fact for Class this is currently not defined in terms of entity_xref/2.
differentium/3	Must be used in conjunction with genus/2.
directed_path_over/2
directed_simple_path_over/2
disjoint_from/2	true if there is nothing that instantiates both Class and DisjointClass.
disjoint_fromS/2	infers symmetric relationships.
disjoint_from_violation/3	true if disjoint_from/2 holds between P1 and P2, and C is a subclass/2 of both.
disjoint_from_violation_nr/3	non-redundant version of disjoint_from_violation/3.
disjoint_over/2
disjoint_over_violation/4	true if X is declared to be disjoint with Y over some relation R, and there is some A that stands in relation R to X and Y.
entailed_by/2	true if Statement is entailed (logically inferred) by Rule Expression may be 'true' if deduction provenance is not maintained.
entailed_by/3
equivalent_class/2	corresponds to owl:equivalentClass.
equivalent_to_chain/2	true if Relation is equivalent the chain of relations in RelationList e.g.
expand_assertion_to/2	OWL macros.
expand_expression_to/2	OWL macros.
genus/2	A logical definition of Class refines Genus via some discriminating characteristic (differentium/3); e.g.
holds_bidirectionally_for/2	holds_bidirectionally_for(SR,R), X SR Y, R inverse_of RI => X R Y and Y RI X DEPRECATED.
holds_bidirectionally_for/3	holds_bidirectionally_for(SR,R,Inv), X SR Y => X R Y and Y Inv X.
holds_for_all_times/1
holds_over_chain/2	true if Relation is transitive over the chain of relations in RelationList e.g.
id_axiom/2	Axiom can be any term.
idspace/2	DPRECATED: use idspace_uri/2 instead.
idspace_mireot/2	true if RefEntity is referenced directly or indirectly from an entity in IDSpace.
idspace_mireot/3	idspace_mireot/2 with the additional constraint that directly referenced entities must come from RefEntityIDSpace.
idspace_references/2	true if Ref is in the parentRT/2 closure of a class in idspace S.
idspace_references_reflexive/2	as idspace_references/2, but includes all classes in S.
inferred_child_via/3	the chain: InferredChild r[1] r[2] ... r[n-1] r[n] Entity must be true, where Over = [r[1], ..., r[n]].
inferred_parent/2
inst/1	true if Instance is declared to be an instance of some class.
inst/2	combines inst/1 and entity_label/2 holds when inst(?Instance) and entity_label(?Instance,?Name).
inst_of/2	true if Instance is a direct instaniation of Class - this represents a 'timeless' instantiation, such as set membership or owl/DL.
inst_ofRT/2	true if Instance is an instance of Class, taking into account transitivity combines inst_of/2 and subclassRT/2.
inst_rel/3	true if Instance stands in Relation to ToInstance - this represents a 'timeless' relationship See also inst_rel/4 to time-indexed relations.
inst_rel_anon/3	true if Instance stands in Relation to some unnamed instance of Class.
inst_rel_type/3	true if I is related by Rel to some instance of type Type.
inst_sv/3	disjunction of inst_sv/4 and inst_rel/3 true if inst_sv(Inst,Relation,Reulatum) or inst_rel(Inst,Relation,Relatum).
inst_sv/4	true if Instance has a Slot with Value, where Value is of DataType.
inverse_of/2	true if Inverse is the inverse of Relation, such that the inverse is held between instances formally: inst_rel(X,R,Y),inverse(R,R1) => inst_rel(Y,R1,X).
inverse_of_on_instance_level/2	true if all_some(Relation,InstRelation),inverse_of(InstRelation,InstRelationInv),all_some(InstRelationInv,Inverse) (always asserted) TODO: DEPRECATE?
is_anonymous/1	true if Entity is unnamed equivalent to bNode in RDF.
is_anti_symmetric/1
is_asymmetric/1
is_class_level/1	Relation only holds between classes: also is non-inheritable.
is_cyclic/1
is_functional/1
is_inverse_functional/1
is_metadata_tag/1	does this relation only hold at the class metadata level?
is_proper/1
is_reflexive/1	formally: forall(X), is_reflexive(R) => X R X.
is_symmetric/1	class level.
is_transitive/1	formally: X R Y, Y R Z, is_transitive(R) => X R Z.
is_unsatisfiable/1	true if Class is defined in such a way it can never be instantiated; for example, being a subclass of two disjoint classes.
lexical_category/2	DEPRECATED.
logicalformula/3	DEPRECATED.
max_cardinality_restriction/4	A relationship between two classes such that all instances of ?Class stand in ?Relation to at most ?Max instance(s) of ?ToClass.
metaproperty/2	reified unary relation predicates.
min_cardinality_restriction/4	A relationship between two classes such that all instances of ?Class stand in ?Relation to at least ?Min instance(s) of ?ToClass.
nochild/1	true if Class is bottom of union of subclass and restriction hierarchy.
nochild/2	true if Class is bottom of union of subclass and restriction hierarchy within Ontologyy.
node_link/3	true if parent/3 or inst_rel/3 TODO: check semantics.
noparent/1	true if Class is top of union of subclass and restriction hierarchy.
noparent/2	true if Class is top of union of subclass and restriction hierarchy within Ontology.
obsolete/3	DEPRECATED: combines entity_label/2, entity_obsolete/1 and belongs/2.
obsolete_class/2	DEPRECATED combines entity_label/2, entity_obsolete/1.
ontol_subgraph/5	Input = ClassList | KVList G = [ChildParentPair1, ....].
ontology/1	e.g.
ontology/2	DEPRECATED see ontology/3 .
ontology/3	DEPRECATED.
parent/2	as parent/3.
parent/3	combines subclass/2 and restriction/3 also genus/2 differentia/3 true if Relation=subclass and subclass(Class,ParentClass) or if restriction(?Class,?Relation,?ParentClass).
parentRT/2	reflexive transitive parent/2.
parentRT/3	reflexive transitive parent/3.
parentT/2	see parentT/3.
parentT/3	transitive parent/3 new: now uses inferred_parent_via/3.
parentT/4	DEPRECATED?
parent_cycle/2	check for cyclical paths, going up from ID a parent is defined by subclass/2 or restriction/3.
parent_over/3	as parent_over/4 DEPRECATED.
parent_over/4	true if ParentClass is a parent of Class by relation R uses subclass/2 rules: X R Y if X subclassRT X1 and X1 R Y1 and Y1 subclassRT Y.
parent_overT/3	transitive closure over parent_over/3 DEPRECATED - this is now the same as parentT/3 and inferred_parent_via/3 with chains of length=1.
parent_over_nr/3	as parent_over_nr/4.
parent_over_nr/4	nonredundant version of parent_over/4.
proper_form_of/2
property/1	holds when Relation is the ID of an entity which defines a relationship which holds between two classes (arg2 of restriction/3) or between two instance (arg2 of inst_rel/3) equivalent to owl:ObjectProperty.
property/2	combines property/1 and entity_label/2 holds when property(?Relation) and entity_label(?Relation,?Name) see entity_label/2.
property_domain/2	all instances that are the subject of Relation instantiate Class.
property_intersection_element/2	we write the relation intersection p^q as two facts property_intersection_element('p^q',p).
property_intersection_elements/2
property_range/2	all instances that are the object of Relation instantiate Class.
property_relationship/3
property_union_element/2	we write the relation union p^q as two facts property_union_element('p^q',p).
property_union_elements/2
range_cardinality_restriction/4
redundant_parent/5
redundant_subclass/3	true if Class is direct subclass/2 of Parent, and Class is a subclassT/2 of Intermediate which is a subclassT/2 of Parent.
referenced_id/2	ID references RefID if RefID appears as object of subclass/restriction/intersection relation.
reflexive_over/2
reification/2	true if Statement identifies the fact Term currently Term must be restriction/3 or inst_rel/3.
relation/1	deprecated: disjunction of property/1 and slot/1 holds if Rel is a property or slot.
restriction/3	A relationship between two classes such that all instances of ?Class stand in ?Relation to some instance of ?ToClass.
restriction/4	ternary relations.
restriction/5	quaternary relations.
strict_subclass/2	true if A is a subclass of B, and there is no Z such that a is a subclass of Z.
subclass/2	An asserted is_a (subtype, subsumption) relationship equivalent to owl:subClassOf transitive form is subclassT/2.
subclassRT/2	reflexive form of subclassT/2.
subclassT/2	transitive form of subclass/2.
subclassX/2	tests if A can be inferred to be a subclass of B.
subclassXT/2	reflexive version of subclassX/2.
subclass_cycle/2	check for cyclical paths, going up from ID.
subclass_lca/2
subclass_underlap/3	C is_a P1 and C is_a P2 P1 and P2 are non-disjoint because o C.
topclass/1	true if Class is top of subclass hierarchy.
topclass/2	true if Class is top of subclass hierarchy within Ontology.
transitive_form_of/2	strictly required?
transitive_over/2	true if Relation is transitive over Over formally: X R Y, Y R1 Z, transitive_over(R,R1) => X R Z.
ontol_entailment_basic.pro
ontol_entailment_inverse.pro
ontol_management.pro
is_nondangling/1
merge_class/2
merge_class/3	merges Src into Tgt.
merge_equivalent_classes/0	assumes pre-reasoned ontology.
ontol_reasoner.pro
explanation/3
explanation/4	true if Text is a RuleName-based natural language explanation for Fact.
show_all_explanations/0
show_all_explanations/1
show_all_explanations/2
show_all_explanations/3
ontol_sqlmap_go.pro
ontol_sqlmap_go_util.pro
ontol_sqlmap_obd.pro
ontol_sqlmap_obd_core.pro
ontol_vizlayout.pro
graph_to_semantic_svg_xml/2
ontol_writer.pro
ontol_writer_chadoxml.pro
ontol_writer_dot.pro
write_edges_to_image/2	generates a png file.
ontol_writer_obo.pro
ontol_writer_text.pro
ontol_writer_thea_syntax.pro
owl_util.pro
parser_obo.pro
rdf_id_util.pro
homol_bridge_from_ontol.pro
homol_bridge_to_ontol.pro
homol_db.pro
homologous_to/2	parent sharing by homologset_member/2, non-reflexive.
homologset/1
homologset_member/2
homologset_member_taxon/3	Composes homologset_member/2 and feature_organism/2.
homologset_taxon/2
homologset_type/2
interspecies_homologous_to/2	as homologous_to/2 different by feature_organism/2, non-reflexive.
interspecies_reflexive_homologous_to/2	as homologous_to/2 different by feature_organism/2, reflexive.
intraspecies_homologous_to/2	as homologous_to/2 same by feature_organism/2.
intraspecies_reflexive_homologous_to/2	as homologous_to/2 same by feature_organism/2, reflexive.
reflexive_homologous_to/2	as homologous_to/2 but includes self-references.
homol_sqlmap_go.pro
homol_xmlmap_homologene.pro
homoltbl_bridge_to_homol.pro
load_phylo.pro
parser_nhx.pro
phylo_bridge_from_taxon.pro
phylo_bridge_to_ontol.pro
phylo_db.pro
is_speciation/1	true if Node represents a speciation event.
iso_orthologous_pair/2	true if A and B are iso-orthologs.
orthologous_pair/2	true if A and B are orthologous (i.e.
paralogous_pair/2	true if A and B are paralogous (i.e.
phylo_rca/2
phylogeny/2
phylonode/1	represents a node in a phylogenetic tree.
phylonode/2	combination of phylonode/1 and entity_label/2.
phylonode/4	DEPRECATED.
phylonode_ancestor_distance/3
phylonode_branchlen/2
phylonode_confidence/3	Type = bootstrap | ....
phylonode_depth/2
phylonode_duplications/2
phylonode_height/2
phylonode_leaf/1	true if Node is parent of nothing.
phylonode_parent/2
phylonode_parentRT/2	reflexive transitive closure of phylonode_parent/2.
phylonode_parentT/2	transitive closure of phylonode_parent/2.
phylonode_root/1	true if Node has no parents.
phylonode_speciations/2
phylonode_taxon/2
phylonode_taxon_ratio/4	| S1 ��� S2| / | S1 ��� S2| where S1 and S2 are the children of Node.
phylonode_tree/2
phylonode_xref/2
phylonodeprop/3
phylotree/1
phylotree_binary/1	true if Tree is binary.
phylotree_monophyletic/2	true if OutGroup is not a descendant of the LCA of Nodes.
phylo_sqlmap_chado.pro
phylo_sqlmap_enscompara.pro
phylo_writer_chadoxml.pro
phylo_xmlmap_phyloxml.pro
taxon_db.pro
taxbinomial/3
taxleaf/1	unifies with all tips of the taxonomy tree.
taxname/2	scientific name.
taxparentT/2	unifies with all ancestors of node ID (ie transitive parent).
biopax3_bridge_from_rdf.pro
biopax3_bridge_to_pathway.pro
biopax3_db.pro
biopax_idspace_replace_rules.pro
load_sb.pro
pathway_db.pro
atomic_event/1	true if E has no sub-events.
entity_db_id/3
event/1	true if E is an event.
event_catalyst/2	as event_catalyst/4.
event_catalyst/3	as event_catalyst/4.
event_catalyst/4	should be renamed event_controller/4?
event_input/2	as event_input/2, without cardinality.
event_input/3	true if event E takes Num copies of M as input.
event_input_molecule/2	composition of event_input/2 and has_leaf_part/2.
event_output/2	see event.
event_output/3	true if event E takes Num copies of M as output.
event_output_molecule/2	composition of event_output/2 and has_leaf_part/2.
event_participant_role/3
event_participating_continuant_roleT/3	Cont participates in E (or a super-event of E) with role Role.
has_leaf_part/2	set of all leaf-nodes in the partonomy for W.
has_part/2
has_part/3
has_partRT/2	reflexive transitive closure of has_partT/2.
has_partT/2	transitive closure of has_partT/2.
has_subtype/2
located_in/2	corresponds to cellularLocation/2 relation between a snapshot and a continuant.
modification_type/2	Type will typically be a CHEBI class ID.
molecule_modification/2	true if snapshot of molecule Mol is distinguished by modification Mod.
part_of/2	inverse of has_part/2.
part_ofT/2	transitive closure of part_of/2.
pathway_initiated_by/3	E1 preceded_by E, E1 is in the P but E is not.
pathway_overlaps/2	pathways overlap if they have events in common.
pathway_partial_overlaps/2	as pathway_overlaps/2, with the additional constraint that neither pathway is part of the other.
preceded_by/2	true if P2 is causally preceded_by P1.
snapshot_continuant/2	maps a state-specific snapshot of an entity (e.g.
snapshot_db_id/3	composes snapshot_continuant/2 and entity_db_id/3.
subpathway_of/2	includes reactions to pathways.
target_type/2	type will typically be a class ID from CHEBI.
transport/4	as transport/6 .
transport/6	true if Event is a transportation reaction with Continuant as cargo.
transport_cargo/2	see transport/6.
transport_chain/3	true if C is a continuant which is passed along sequentially along the locations in LL via the events in PL.
transport_destination/2	see transport/6.
transport_source/2	see transport/6.
sb_bridge_from_biopax.pro
sb_bridge_from_biopax_level2.pro
sb_db.pro
annotation/4
assignment_rule/2
compartment/2
compartment_class/2	mode: nondet ID for an ontol class for this compartment; eg a GO ID or a KEGG ID.
component_of/2
kinetic_law/2
model/2
model_class/2	mode: nondet ID for an ontol class for this model; eg a GO ID or a KEGG ID.
parameter/4
reaction/2
reaction_link/2
reaction_link/3	two reactions directly linked via a connecting species (excludes modifiers).
reaction_modifier/2	relation between a biochemical reaction and a molecular constituent that plays a role in the process but is unmodified .
reaction_participant/2	contracted form of reaction_participant/2.
reaction_participant/3
reaction_product/2	relation between a biochemical reaction and a molecular constituent produced in the reaction.
reaction_reactant/2	relation between a biochemical reaction and a molecular constituent that is consumed in the reaction.
sbentity/2
sbentity/3	mode: nondet any sbentity: species, compartment or reaction.
sbentity_class/2	mode: nondet ID for an ontol class for this sbentity; sbentity can be a species, model, compartment or reaction.
sbentity_param/3
species/3
species_class/2	ID for an ontol class for this species; eg a ChEBI ID or a KEGG ID.
species_path/3	finds path between an input species and an output species.
unit/4
unitdef/2
sb_writer_chadoxml.pro
sb_writer_dot.pro
sb_xmlmap_sbml.pro
serval.pro
append_session_data/4
start_server/1	starts a server on a specified port.
submit_param/2	nondet.
write_sterm/3	evaluates an html function term, writing html/xml as a side-effect.
load_sql.pro
rdb_util.pro
rdb_connect/2	mode:semidet.
rdb_handle/2
rdb_lookup/2	mode:nondet.
rdb_query/2	DEPRECATEd??? mode:nondet.
rdb_query/3	mode:nondet.
sqlbind/1	BindArgs = Module:PredicateSpec-DB or Module:PredicateSpec.
sqlbind/2	rewrites Predicate to a SQL call on DB.
sql_compiler.pro
get_type/2	Prolog implementation specific definition of type retrieval sepia Prolog version given here.
load_schema_defs/1	loads a schema into memory, allowing sql_compiler to make use of it for plterm_to_sqlterm/3.
plterm_to_sqlterm/3	rewrite a prolog goal as a SQL Term.
rewrite_query/2
sqlterm2atom/2	translates an SQL Term to an atom that conforms to SQL syntax.
schema_chado.pro
schema_enscompara.pro
schema_enscompara52.pro
schema_enscore44.pro
	Ensembl Core Schema Mapping
alt_allele/2	maps to sql table.
analysis/14	maps to sql table.
analysis_description/5	maps to sql table.
assembly/7	maps to sql table.
assembly_exception/9	maps to sql table.
attrib_type/4	maps to sql table.
coord_system/5	maps to sql table.
density_feature/6	maps to sql table.
density_type/5	maps to sql table.
ditag/5	maps to sql table.
ditag_feature/13	maps to sql table.
dna/2	maps to sql table.
dna_align_feature/14	maps to sql table.
dnac/3	maps to sql table.
exon/8	maps to sql table.
exon_stable_id/5	maps to sql table.
exon_transcript/3	maps to sql table.
external_db/9	maps to sql table.
external_synonym/2	maps to sql table.
gene/12	maps to sql table.
gene_archive/8	maps to sql table.
gene_attrib/3	maps to sql table.
gene_stable_id/5	maps to sql table.
go_xref/2	maps to sql table.
identity_xref/11	maps to sql table.
interpro/2	maps to sql table.
karyotype/6	maps to sql table.
map/2	maps to sql table.
mapping_session/8	maps to sql table.
marker/8	maps to sql table.
marker_feature/7	maps to sql table.
marker_map_location/6	maps to sql table.
marker_synonym/4	maps to sql table.
meta/3	maps to sql table.
meta_coord/3	maps to sql table.
misc_attrib/3	maps to sql table.
misc_feature/5	maps to sql table.
misc_feature_misc_set/2	maps to sql table.
misc_set/5	maps to sql table.
object_xref/4	maps to sql table.
oligo_array/5	maps to sql table.
oligo_feature/8	maps to sql table.
oligo_probe/6	maps to sql table.
peptide_archive/3	maps to sql table.
prediction_exon/10	maps to sql table.
prediction_transcript/7	maps to sql table.
protein_align_feature/13	maps to sql table.
protein_feature/11	maps to sql table.
qtl/6	maps to sql table.
qtl_feature/5	maps to sql table.
qtl_synonym/4	maps to sql table.
regulatory_factor/3	maps to sql table.
regulatory_factor_coding/3	maps to sql table.
regulatory_feature/8	maps to sql table.
regulatory_feature_object/5	maps to sql table.
regulatory_search_region/9	maps to sql table.
repeat_consensus/5	maps to sql table.
repeat_feature/10	maps to sql table.
seq_region/4	maps to sql table.
seq_region_attrib/3	maps to sql table.
simple_feature/8	maps to sql table.
stable_id_event/7	maps to sql table.
supporting_feature/3	maps to sql table.
transcript/12	maps to sql table.
transcript_attrib/3	maps to sql table.
transcript_stable_id/5	maps to sql table.
transcript_supporting_feature/3	maps to sql table.
translation/6	maps to sql table.
translation_attrib/3	maps to sql table.
translation_stable_id/5	maps to sql table.
unconventional_transcript_association/3	maps to sql table.
unmapped_object/11	maps to sql table.
unmapped_reason/3	maps to sql table.
xref/8	maps to sql table.
schema_enscore51.pro
schema_go.pro
schema_obd.pro
stats_distributions.pro
hypergeometric/5
logNCr/3
log_factorial/2
p_value_by_hypergeometric/5	Suppose that we have a total population of N genes, in which M have a particular annotation.
load_web.pro
web_fetch.pro
web_fetch/3
web_fetch/4	== web_fetch(ncbi,[service=efetch,db=omim,id=601100,retmode=xml,rettype=full],Results) ==.
web_fetch_cancergrid.pro
web_search_cancergrid/3
web_search_cancergrid/4
web_fetch_google.pro
web_search_google/2	queries google based on search atom.
web_search_google/3	As web_search_google/2, with the following allowed options:.
web_fetch_ncbi.pro
gilist_to_accmap/2	given a list of GI numbers, return a map from GI numbers to accessions.
web_search_ncbi/3	== web_search_ncbi(homologene,query('BRCA1','gene name'),Results) ==.
web_fetch_yahoo.pro
web_search_expander.pro
xml_transform.pro
apply_xmlpred/3	mode: det transform an XML tree into a list of flat terms that can then be asserted as data predicates.
pxpath/3
xml_compact_to_full/2	turns compact syntax into sgml-module representations.
xml_writer.pro
doc_start/1	DEPRECATED SYNONYM for xmldoc_start/1 *.
xmldoc_start/1	*.
xmlnode_end/2	det.
xmlnode_end/3	det.
xmlnode_start/3	det.
xmlnode_start/4	det.
pldoc-server
pldoc_modules_std.pro