class LexicalMapEngine():
"""
generates lexical matches between pairs of ontology classes
"""
SCORE = 'score'
LEXSCORE = 'lexscore'
SIMSCORES = 'simscores'
CONDITIONAL_PR = 'cpr'
def __init__(self, wsmap=default_wsmap(), config=None):
"""
Arguments
---------
wdmap: dict
maps words to normalized synonyms.
config: dict
A configuration conforming to LexicalMapConfigSchema
"""
# maps label or syn value to Synonym object
self.lmap = {}
# maps node id to synonym objects
self.smap = {}
self.wsmap = wsmap
self.npattern = re.compile('[\W_]+')
self.exclude_obsolete = True
self.ontology_pairs = None
self.id_to_ontology_map = defaultdict(list)
self.merged_ontology = Ontology()
self.config = config if config is not None else {}
self.stats = {}
def index_ontologies(self, onts):
logging.info('Indexing: {}'.format(onts))
for ont in onts:
self.index_ontology(ont)
def index_ontology(self, ont):
"""
Adds an ontology to the index
This iterates through all labels and synonyms in the ontology, creating an index
"""
self.merged_ontology.merge([ont])
syns = ont.all_synonyms(include_label=True)
include_id = self._is_meaningful_ids()
logging.info("Include IDs as synonyms: {}".format(include_id))
if include_id:
for n in ont.nodes():
v = n
# Get fragment
if v.startswith('http'):
v = re.sub('.*/', '', v)
v = re.sub('.*#', '', v)
syns.append(Synonym(n, val=v, pred='label'))
logging.info("Indexing {} syns in {}".format(len(syns), ont))
logging.info("Distinct lexical values: {}".format(len(
self.lmap.keys())))
for syn in syns:
self.index_synonym(syn, ont)
for nid in ont.nodes():
self.id_to_ontology_map[nid].append(ont)
def label(self, nid):
return self.merged_ontology.label(nid)
def index_synonym(self, syn, ont):
"""
Index a synonym
Typically not called from outside this object; called by `index_ontology`
"""
if not syn.val:
if syn.pred == 'label':
if not self._is_meaningful_ids():
if not ont.is_obsolete(syn.class_id):
pass
#logging.error('Use meaningful ids if label not present: {}'.format(syn))
else:
logging.warning("Incomplete syn: {}".format(syn))
return
if self.exclude_obsolete and ont.is_obsolete(syn.class_id):
return
syn.ontology = ont
prefix, _ = ont.prefix_fragment(syn.class_id)
v = syn.val
caps_match = re.match('[A-Z]+', v)
if caps_match:
# if > 75% of length is caps, assume abbreviation
if caps_match.span()[1] >= len(v) / 3:
syn.is_abbreviation(True)
# chebi 'synonyms' are often not real synonyms
# https://github.com/ebi-chebi/ChEBI/issues/3294
if not re.match('.*[a-zA-Z]', v):
if prefix != 'CHEBI':
logging.warning('Ignoring suspicous synonym: {}'.format(syn))
return
v = self._standardize_label(v)
# TODO: do this once ahead of time
wsmap = {}
for w, s in self.wsmap.items():
wsmap[w] = s
for ss in self._get_config_val(prefix, 'synsets', []):
# TODO: weights
wsmap[ss['synonym']] = ss['word']
nv = self._normalize_label(v, wsmap)
self._index_synonym_val(syn, v)
nweight = self._get_config_val(prefix, 'normalized_form_confidence',
0.8)
if nweight > 0 and not syn.is_abbreviation():
if nv != v:
nsyn = Synonym(syn.class_id,
val=syn.val,
pred=syn.pred,
lextype=syn.lextype,
ontology=ont,
confidence=syn.confidence * nweight)
self._index_synonym_val(nsyn, nv)
def _index_synonym_val(self, syn, v):
lmap = self.lmap
smap = self.smap
cid = syn.class_id
if v not in lmap:
lmap[v] = []
lmap[v].append(syn)
if cid not in smap:
smap[cid] = []
smap[cid].append(syn)
def _standardize_label(self, v):
# Add spaces separating camelcased strings
v = re.sub('([a-z])([A-Z])', r'\1 \2', v)
# always use lowercase when comparing
# we may want to make this configurable in future
v = v.lower()
return v
def _normalize_label(self, s, wsmap):
"""
normalized form of a synonym
"""
toks = []
for tok in list(set(self.npattern.sub(' ', s).split(' '))):
if tok in wsmap:
tok = wsmap[tok]
if tok != "":
toks.append(tok)
toks.sort()
return " ".join(toks)
def _get_config_val(self, prefix, k, default=None):
v = None
for oc in self.config.get('ontology_configurations', []):
if prefix == oc.get('prefix', ''):
v = oc.get(k, None)
if v is None:
v = self.config.get(k, None)
if v is None:
v = default
return v
def _is_meaningful_ids(self):
return self.config.get('meaningful_ids', False)
def find_equiv_sets(self):
return self.lmap
def get_xref_graph(self):
"""
Generate mappings based on lexical properties and return as nx graph.
Algorithm
~~~~~~~~~
- A dictionary is stored between ref:`Synonym` values and synonyms. See ref:`index_synonym`.
Note that Synonyms include the primary label
- Each key in the dictionary is examined to determine if there exist two Synonyms from
different ontology classes
This avoids N^2 pairwise comparisons: instead the time taken is linear
After initial mapping is made, additional scoring is performed on each mapping
Edge properties
~~~~~~~~~~~~~~~
The return object is a nx graph, connecting pairs of ontology classes.
Edges are annotated with metadata about how the match was found:
syns: pair
pair of `Synonym` objects, corresponding to the synonyms for the two nodes
score: int
score indicating strength of mapping, between 0 and 100
Returns
-------
Graph
nx graph (bidirectional)
"""
# initial graph; all matches
g = nx.MultiDiGraph()
# lmap collects all syns by token
items = self.lmap.items()
logging.info("collecting initial xref graph, items={}".format(
len(items)))
i = 0
sum_nsyns = 0
n_skipped = 0
has_self_comparison = False
if self.ontology_pairs:
for (o1id, o2id) in self.ontology_pairs:
if o1id == o2id:
has_self_comparison = True
for (v, syns) in items:
sum_nsyns += len(syns)
i += 1
if i % 1000 == 1:
logging.info(
'{}/{} lexical items avgSyns={}, skipped={}'.format(
i, len(items), sum_nsyns / len(items), n_skipped))
if len(syns) < 2:
n_skipped += 1
next
if len(syns) > 10:
logging.info('Syns for {} = {}'.format(v, len(syns)))
for s1 in syns:
s1oid = s1.ontology.id
s1cid = s1.class_id
for s2 in syns:
# optimization step: although this is redundant with _is_comparable,
# we avoid inefficient additional calls
if s1oid == s2.ontology.id and not has_self_comparison:
next
if s1cid != s2.class_id:
if self._is_comparable(s1, s2):
g.add_edge(s1.class_id, s2.class_id, syns=(s1, s2))
logging.info("getting best supporting synonym pair for each match")
# graph of best matches
xg = nx.Graph()
for i in g.nodes():
for j in g.neighbors(i):
best = 0
bestm = None
for m in g.get_edge_data(i, j).values():
(s1, s2) = m['syns']
score = self._combine_syns(s1, s2)
if score > best:
best = score
bestm = m
syns = bestm['syns']
xg.add_edge(i,
j,
score=best,
lexscore=best,
syns=syns,
idpair=(i, j))
self.score_xrefs_by_semsim(xg)
self.assign_best_matches(xg)
if self.merged_ontology.xref_graph is not None:
self.compare_to_xrefs(xg, self.merged_ontology.xref_graph)
else:
logging.error("No xref graph for merged ontology")
logging.info("finished xref graph")
return xg
# true if syns s1 and s2 should be compared.
# - if ontology_pairs is set, then only consider (s1,s2) if their respective source ontologies are in the list of pairs
# - otherwise compare all classes, but only in one direction
def _is_comparable(self, s1, s2):
if s1.class_id == s2.class_id:
return False
if self.ontology_pairs is not None:
#logging.debug('TEST: {}{} in {}'.format(s1.ontology.id, s2.ontology.id, self.ontology_pairs))
return (s1.ontology.id, s2.ontology.id) in self.ontology_pairs
else:
return s1.class_id < s2.class_id
def _blanket(self, nid):
nodes = set()
for ont in self.id_to_ontology_map[nid]:
nodes.update(ont.ancestors(nid))
nodes.update(ont.descendants(nid))
return list(nodes)
def score_xrefs_by_semsim(self, xg, ont=None):
"""
Given an xref graph (see ref:`get_xref_graph`), this will adjust scores based on
the semantic similarity of matches.
"""
logging.info(
"scoring xrefs by semantic similarity for {} nodes in {}".format(
len(xg.nodes()), ont))
for (i, j, d) in xg.edges(data=True):
pfx1 = self._id_to_ontology(i)
pfx2 = self._id_to_ontology(j)
ancs1 = self._blanket(i)
ancs2 = self._blanket(j)
s1, _, _ = self._sim(xg, ancs1, ancs2, pfx1, pfx2)
s2, _, _ = self._sim(xg, ancs2, ancs1, pfx2, pfx1)
s = 1 - ((1 - s1) * (1 - s2))
logging.debug("Score {} x {} = {} x {} = {} // {}".format(
i, j, s1, s2, s, d))
xg[i][j][self.SIMSCORES] = (s1, s2)
xg[i][j][self.SCORE] *= s
def _sim(self, xg, ancs1, ancs2, pfx1, pfx2):
"""
Compare two lineages
"""
xancs1 = set()
for a in ancs1:
if a in xg:
# TODO: restrict this to neighbors in single ontology
for n in xg.neighbors(a):
pfx = self._id_to_ontology(n)
if pfx == pfx2:
xancs1.add(n)
logging.debug('SIM={}/{} ## {}'.format(len(xancs1.intersection(ancs2)),
len(xancs1),
xancs1.intersection(ancs2),
xancs1))
n_shared = len(xancs1.intersection(ancs2))
n_total = len(xancs1)
return (1 + n_shared) / (1 + n_total), n_shared, n_total
# given an ontology class id,
# return map keyed by ontology id, value is a list of (score, ext_class_id) pairs
def _neighborscores_by_ontology(self, xg, nid):
xrefmap = defaultdict(list)
for x in xg.neighbors(nid):
score = xg[nid][x][self.SCORE]
for ont in self.id_to_ontology_map[x]:
xrefmap[ont.id].append((score, x))
return xrefmap
# normalize direction
def _dirn(self, edge, i, j):
if edge['idpair'] == (i, j):
return 'fwd'
elif edge['idpair'] == (j, i):
return 'rev'
else:
return None
def _id_to_ontology(self, id):
return self.merged_ontology.prefix(id)
#onts = self.id_to_ontology_map[id]
#if len(onts) > 1:
# logging.warning(">1 ontology for {}".format(id))
def compare_to_xrefs(self, xg1, xg2):
"""
Compares a base xref graph with another one
"""
ont = self.merged_ontology
for (i, j, d) in xg1.edges(data=True):
ont_left = self._id_to_ontology(i)
ont_right = self._id_to_ontology(j)
unique_lr = True
num_xrefs_left = 0
same_left = False
if i in xg2:
for j2 in xg2.neighbors(i):
ont_right2 = self._id_to_ontology(j2)
if ont_right2 == ont_right:
unique_lr = False
num_xrefs_left += 1
if j2 == j:
same_left = True
unique_rl = True
num_xrefs_right = 0
same_right = False
if j in xg2:
for i2 in xg2.neighbors(j):
ont_left2 = self._id_to_ontology(i2)
if ont_left2 == ont_left:
unique_rl = False
num_xrefs_right += 1
if i2 == i:
same_right = True
(x, y) = d['idpair']
xg1[x][y]['left_novel'] = num_xrefs_left == 0
xg1[x][y]['right_novel'] = num_xrefs_right == 0
xg1[x][y]['left_consistent'] = same_left
xg1[x][y]['right_consistent'] = same_right
def assign_best_matches(self, xg):
"""
For each node in the xref graph, tag best match edges
"""
logging.info("assigning best matches for {} nodes".format(
len(xg.nodes())))
for i in xg.nodes():
xrefmap = self._neighborscores_by_ontology(xg, i)
for (ontid, score_node_pairs) in xrefmap.items():
score_node_pairs.sort(reverse=True)
(best_score, best_node) = score_node_pairs[0]
logging.info("BEST for {}: {} in {} from {}".format(
i, best_node, ontid, score_node_pairs))
edge = xg[i][best_node]
dirn = self._dirn(edge, i, best_node)
best_kwd = 'best_' + dirn
if len(score_node_pairs
) == 1 or score_node_pairs[0] > score_node_pairs[1]:
edge[best_kwd] = 2
else:
edge[best_kwd] = 1
for (score, j) in score_node_pairs:
edge_ij = xg[i][j]
dirn_ij = self._dirn(edge_ij, i, j)
edge_ij['cpr_' + dirn_ij] = score / sum(
[s for s, _ in score_node_pairs])
for (i, j, edge) in xg.edges(data=True):
# reciprocal score is set if (A) i is best for j, and (B) j is best for i
rs = 0
if 'best_fwd' in edge and 'best_rev' in edge:
rs = edge['best_fwd'] * edge['best_rev']
edge['reciprocal_score'] = rs
edge['cpr'] = edge['cpr_fwd'] * edge['cpr_rev']
def _best_match_syn(self, sx, sys, scope_map):
"""
The best match is determined by the highest magnitude weight
"""
SUBSTRING_WEIGHT = 0.2
WBEST = None
sbest = None
sxv = self._standardize_label(sx.val)
sxp = self._id_to_ontology(sx.class_id)
for sy in sys:
syv = self._standardize_label(sy.val)
syp = self._id_to_ontology(sy.class_id)
W = None
if sxv == syv:
confidence = sx.confidence * sy.confidence
if sx.is_abbreviation() or sy.is_abbreviation:
confidence *= self._get_config_val(
sxp, 'abbreviation_confidence', 0.5)
confidence *= self._get_config_val(
syp, 'abbreviation_confidence', 0.5)
W = scope_map[sx.scope()][sy.scope()] + logit(confidence / 2)
elif sxv in syv:
W = np.array((-SUBSTRING_WEIGHT, SUBSTRING_WEIGHT, 0, 0))
elif syv in sxv:
W = np.array((SUBSTRING_WEIGHT, -SUBSTRING_WEIGHT, 0, 0))
if W is not None:
# The best match is determined by the highest magnitude weight
if WBEST is None or max(abs(W)) > max(abs(WBEST)):
WBEST = W
sbest = sy
return WBEST, sbest
def weighted_axioms(self, x, y, xg):
"""
return a tuple (sub,sup,equiv,other) indicating estimated prior probabilities for an interpretation of a mapping
between x and y.
See kboom paper
"""
# TODO: allow additional weighting
# weights are log odds w=log(p/(1-p))
# (Sub,Sup,Eq,Other)
scope_pairs = [('label', 'label', 0.0, 0.0, 3.0, -0.8),
('label', 'exact', 0.0, 0.0, 2.5, -0.5),
('label', 'broad', -1.0, 1.0, 0.0, 0.0),
('label', 'narrow', 1.0, -1.0, 0.0, 0.0),
('label', 'related', 0.0, 0.0, 0.0, 0.0),
('exact', 'exact', 0.0, 0.0, 2.5, -0.5),
('exact', 'broad', -1.0, 1.0, 0.0, 0.0),
('exact', 'narrow', 1.0, -1.0, 0.0, 0.0),
('exact', 'related', 0.0, 0.0, 0.0, 0.0),
('related', 'broad', -0.5, 0.5, 0.0, 0.0),
('related', 'narrow', 0.5, -0.5, 0.0, 0.0),
('related', 'related', 0.0, 0.0, 0.0, 0.0),
('broad', 'broad', 0.0, 0.0, 0.0, 1.0),
('broad', 'narrow', -0.5, 0.5, 0.0, 0.2),
('narrow', 'narrow', 0.0, 0.0, 0.0, 0.0)]
# populate symmetric lookup matrix
scope_map = defaultdict(dict)
for (l, r, w1, w2, w3, w4) in scope_pairs:
l = l.upper()
r = r.upper()
scope_map[l][r] = np.array((w1, w2, w3, w4))
scope_map[r][l] = np.array((w2, w1, w3, w4))
# TODO: get prior based on ontology pair
# cumulative sum of weights
WS = None
pfx1 = self._id_to_ontology(x)
pfx2 = self._id_to_ontology(y)
for mw in self.config.get('match_weights', []):
mpfx1 = mw.get('prefix1', '')
mpfx2 = mw.get('prefix2', '')
X = np.array(mw['weights'])
if mpfx1 == pfx1 and mpfx2 == pfx2:
WS = X
elif mpfx2 == pfx1 and mpfx1 == pfx2:
WS = self._flipweights(X)
elif mpfx1 == pfx1 and mpfx2 == '' and WS is None:
WS = X
elif mpfx2 == pfx1 and mpfx1 == '' and WS is None:
WS = self._flipweights(X)
if WS is None:
WS = np.array((0.0, 0.0, 0.0, 0.0))
# defaults
WS += np.array(
self.config.get('default_weights', [0.0, 0.0, 1.5, -0.1]))
logging.info('WS defaults={}'.format(WS))
for xw in self.config.get('xref_weights', []):
left = xw.get('left', '')
right = xw.get('right', '')
X = np.array(xw['weights'])
if x == left and y == right:
WS += X
logging.info('MATCH: {} for {}-{}'.format(X, x, y))
elif y == left and x == right:
WS += self._flipweights(X)
logging.info('IMATCH: {}'.format(X))
smap = self.smap
# TODO: symmetrical
WT = np.array((0.0, 0.0, 0.0, 0.0))
WBESTMAX = np.array((0.0, 0.0, 0.0, 0.0))
n = 0
for sx in smap[x]:
WBEST, _ = self._best_match_syn(sx, smap[y], scope_map)
if WBEST is not None:
WT += WBEST
n += 1
if max(abs(WBEST)) > max(abs(WBESTMAX)):
WBESTMAX = WBEST
for sy in smap[y]:
WBEST, _ = self._best_match_syn(sy, smap[x], scope_map)
if WBEST is not None:
WT += WBEST
n += 1
# average best match
if n > 0:
logging.info('Adding BESTMAX={}'.format(WBESTMAX))
WS += WBESTMAX
# TODO: xref, many to many
WS += self._graph_weights(x, y, xg)
# TODO: include additional defined weights, eg ORDO
logging.info('Adding WS, gw={}'.format(WS))
# jaccard similarity
(ss1, ss2) = xg[x][y][self.SIMSCORES]
WS[3] += ((1 - ss1) + (1 - ss2)) / 2
# reciprocal best hits are higher confidence of equiv
rs = xg[x][y]['reciprocal_score']
if rs == 4:
WS[2] += 0.5
if rs == 0:
WS[2] -= 0.2
#P = np.expit(WS)
P = 1 / (1 + np.exp(-WS))
logging.info('Final WS={}, init P={}'.format(WS, P))
# probs should sum to 1.0
P = P / np.sum(P)
return P
def _graph_weights(self, x, y, xg):
ont = self.merged_ontology
xancs = ont.ancestors(x)
yancs = ont.ancestors(y)
pfx = self._id_to_ontology(x)
pfy = self._id_to_ontology(y)
xns = [
n for n in xg.neighbors(y)
if n != x and pfx == self._id_to_ontology(n)
]
yns = [
n for n in xg.neighbors(x)
if n != y and pfy == self._id_to_ontology(n)
]
pweight = 1.0
W = np.array((0, 0, 0, 0))
card = '11'
if len(xns) > 0:
card = 'm1'
for x2 in xns:
if x2 in xancs:
W[0] += pweight
if x in ont.ancestors(x2):
W[1] += pweight
if len(yns) > 0:
if card == '11':
card = '1m'
else:
card = 'mm'
for y2 in yns:
if y2 in yancs:
W[1] += pweight
if y in ont.ancestors(y2):
W[0] += pweight
logging.debug('CARD: {}/{} <-> {}/{} = {} // X={} Y={} // W={}'.format(
x, pfx, y, pfy, card, xns, yns, W))
invcard = card
if card == '1m':
invcard = 'm1'
elif card == 'm1':
invcard = '1m'
CW = None
DEFAULT_CW = None
for cw in self.config.get('cardinality_weights', []):
if 'prefix1' not in cw and 'prefix2' not in cw:
if card == cw['cardinality']:
DEFAULT_CW = np.array(cw['weights'])
if invcard == cw['cardinality']:
DEFAULT_CW = self._flipweights(np.array(cw['weights']))
if 'prefix1' in cw and 'prefix2' in cw:
if pfx == cw['prefix1'] and pfy == cw[
'prefix2'] and card == cw['cardinality']:
CW = np.array(cw['weights'])
if pfx == cw['prefix2'] and pfy == cw[
'prefix1'] and invcard == cw['cardinality']:
CW = self._flipweights(np.array(cw['weights']))
if CW is None:
if DEFAULT_CW is not None:
CW = DEFAULT_CW
else:
if card == '11':
CW = np.array((0.0, 0.0, 1.0, 0.0))
elif card == '1m':
CW = np.array((0.6, 0.4, 0.0, 0.0))
elif card == 'm1':
CW = np.array((0.4, 0.6, 0.0, 0.0))
elif card == 'mm':
CW = np.array((0.2, 0.2, 0.0, 0.5))
return W + CW
def _flipweights(self, W):
return np.array((W[1], W[0], W[2], W[3]))
def grouped_mappings(self, id):
"""
return all mappings for a node, grouped by ID prefix
"""
g = self.get_xref_graph()
m = {}
for n in g.neighbors(id):
[prefix, local] = n.split(':')
if prefix not in m:
m[prefix] = []
m[prefix].append(n)
return m
def unmapped_nodes(self, xg, rs_threshold=0):
unmapped_set = set()
for nid in self.merged_ontology.nodes():
if nid in xg:
for (j, edge) in xg[nid].items():
rs = edge.get('reciprocal_score', 0)
if rs < rs_threshold:
unmapped_set.add(nid)
else:
unmapped_set.add(nid)
return unmapped_set
def unmapped_dataframe(self, xg, **args):
unodes = self.unmapped_nodes(xg, **args)
ont = self.merged_ontology
eg = ont.equiv_graph()
items = []
for n in unodes:
mapped_equivs = ''
if n in eg:
equivs = set(eg.neighbors(n))
mapped_equivs = list(equivs - unodes)
items.append(
dict(id=n, label=ont.label(n), mapped_equivs=mapped_equivs))
df = pd.DataFrame(items, columns=['id', 'label', 'mapped_equivs'])
df = df.sort_values(["id"])
return df
# scores a pairwise combination of synonyms. This will be a mix of
# * individual confidence in the synonyms themselves
# * confidence of equivalence based on scopes
# TODO: unify this with probabilistic calculation
def _combine_syns(self, s1, s2):
cpred = self._combine_preds(s1.pred, s2.pred)
s = self._pred_score(cpred)
s *= s1.confidence * s2.confidence
if s1.is_abbreviation() or s2.is_abbreviation():
s *= self._get_config_val(self._id_to_ontology(s1.class_id),
'abbreviation_confidence', 0.5)
s *= self._get_config_val(self._id_to_ontology(s1.class_id),
'abbreviation_confidence', 0.5)
logging.debug("COMBINED: {} + {} = {}/{}".format(s1, s2, cpred, s))
return round(s)
def _rollup(self, p):
if p == 'label':
return LABEL_OR_EXACT
if p == 'hasExactSynonym':
return LABEL_OR_EXACT
return p
def _combine_preds(self, p1, p2):
if p1 == p2:
return p1
if self._rollup(p1) == self._rollup(p2):
return self._rollup(p1)
return p1 + p2
## TODO: allow this to be weighted by ontology
def _pred_score(self, p):
if p == 'label':
return 100
if p == LABEL_OR_EXACT:
return 90
if p == 'hasExactSynonym':
return 90
return 50
def _in_clique(self, x, cliques):
for s in cliques:
if x in s:
return s
return set()
def as_dataframe(self, xg):
cliques = self.cliques(xg)
ont = self.merged_ontology
items = []
for (x, y, d) in xg.edges(data=True):
# xg is a non-directional Graph object.
# to get a deterministic ordering we use the idpair key
(x, y) = d['idpair']
(s1, s2) = d['syns']
(ss1, ss2) = d['simscores']
clique = self._in_clique(x, cliques)
#ancs = nx.ancestors(g,x)
left_label = ont.label(x)
right_label = ont.label(y)
if ont.is_obsolete(x) and not left_label.startwith('obsolete'):
left_label = "obsolete " + left_label
if ont.is_obsolete(y) and not right_label.startwith('obsolete'):
right_label = "obsolete " + right_label
P = self.weighted_axioms(x, y, xg)
item = {
'left': x,
'left_label': left_label,
'right': y,
'right_label': right_label,
'score': d['score'],
'left_match_type': s1.pred,
'right_match_type': s2.pred,
'left_match_val': s1.val,
'right_match_val': s2.val,
'left_simscore': ss1,
'right_simscore': ss2,
'reciprocal_score': d.get('reciprocal_score', 0),
'conditional_pr_equiv': d.get('cpr'),
'pr_subClassOf': P[0],
'pr_superClassOf': P[1],
'pr_equivalentTo': P[2],
'pr_other': P[3],
'left_novel': d.get('left_novel'),
'right_novel': d.get('right_novel'),
'left_consistent': d.get('left_consistent'),
'right_consistent': d.get('right_consistent'),
'equiv_clique_size': len(clique)
}
items.append(item)
ix = [
'left', 'left_label', 'right', 'right_label', 'left_match_type',
'right_match_type', 'left_match_val', 'right_match_val', 'score',
'left_simscore', 'right_simscore', 'reciprocal_score',
'conditional_pr_equiv', 'pr_subClassOf', 'pr_superClassOf',
'pr_equivalentTo', 'pr_other', 'left_novel', 'right_novel',
'left_consistent', 'right_consistent', 'equiv_clique_size'
]
df = pd.DataFrame(items, columns=ix)
df = df.sort_values(["left", "score", "right"])
return df
def cliques(self, xg):
"""
Return all equivalence set cliques, assuming each edge in the xref graph is treated as equivalent,
and all edges in ontology are subClassOf
Arguments
---------
xg : Graph
an xref graph
Returns
-------
list of sets
"""
g = nx.DiGraph()
for (x, y) in self.merged_ontology.get_graph().edges():
g.add_edge(x, y)
for (x, y) in xg.edges():
g.add_edge(x, y)
g.add_edge(y, x)
return list(strongly_connected_components(g))
def main():
"""
Wrapper for OGR
"""
parser = argparse.ArgumentParser(description='Wrapper for ontobio lexical mapping'
"""
Lexically maps one or more ontologies. Ontologies can be local or remote,
any input handle can be specified, see docs for more details on handles.
If multiple ontologies are specified, then each ontology in the list is compared against the first one.
If a simgle ontology is specified, then all pairs in that ontology will be compared
Output format to be documented - see lexmap.py for the various scoring attributes for now.
""",
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('-o', '--outfile', type=str, nargs='*', default=[], required=False,
help='Path to output file')
parser.add_argument('-t', '--to', type=str, required=False, default='tsv',
help='Output to (tree, dot, ...)')
parser.add_argument('-l', '--labels', type=str,
help='If set, then include node labels in results. DEPRECATED')
parser.add_argument('-s', '--scoring', default='sim', type=str,
help='Score weighting scheme. Default=sim')
parser.add_argument('-P', '--prefix', type=str, required=False,
help='Prefix to constrain traversal on, e.g. PATO, ENVO')
parser.add_argument('-c', '--config', type=str, required=False,
help='lexmap configuration file (yaml). See schema for details')
parser.add_argument('-X', '--xref_weights', type=str, required=False,
help='csv of curated per-xref weights')
parser.add_argument('-u', '--unmapped', type=str, required=False,
help='File to export unmapped nodes to')
parser.add_argument('-A', '--all-by-all', dest='all_by_all', action='store_true',
help='compare all ontologies against all.')
parser.add_argument('-v', '--verbosity', default=0, action='count',
help='Increase output verbosity')
parser.add_argument('ontologies',nargs='*',
help='one or more ontologies to be aligned. Any input handle can be specified')
args = parser.parse_args()
if args.verbosity >= 2:
logging.basicConfig(level=logging.DEBUG)
elif args.verbosity == 1:
logging.basicConfig(level=logging.INFO)
else:
logging.basicConfig(level=logging.WARNING)
logging.info("Welcome!")
factory = OntologyFactory()
onts = [filter_by_prefix(factory.create(h)) for h in args.ontologies]
config = {}
if args.config is not None:
f = open(args.config,'r')
config = yaml.load(f)
f.close()
if args.xref_weights is not None:
if 'xref_weights' not in config:
config['xref_weights'] = []
xws = config['xref_weights']
df = pd.read_csv(args.xref_weights)
df = df.fillna(0.0)
for _, row in df.iterrows():
w = float(row['weight'])
WA = np.array((0.0, 0.0, 0.0, 0.0))
if w < 0:
WA[2] = w
WA[3] = abs(w)
else:
WA[2] = w
WA[3] = -w
xws.append({'left':row['left'],
'right':row['right'],
'weights':WA})
logging.info("ALL: {}".format(args.all_by_all))
lexmap = LexicalMapEngine(config=config)
if len(onts) == 0:
raise ValueException("must pass one or more ontologies")
else:
logging.info("Indexing ontologies: {}".format(onts))
for ont in onts:
lexmap.index_ontology(ont)
oid0 = onts[0].id
pairs = [(oid0,oid0)]
if len(onts) > 1:
if args.all_by_all:
logging.info("All vs ALL: {}".format(onts))
pairs = []
for i in onts:
for j in onts:
if i.id < j.id:
pairs.append((i.id, j.id))
else:
logging.info("All vs first in list: {}".format(oid0))
pairs = [(oid0, ont.id) for ont in onts[1:]]
logging.info("Comparing the following pairs of ontologies: {}".format(pairs))
lexmap.ontology_pairs = pairs
mo = Ontology()
mo.merge(onts)
g = lexmap.get_xref_graph()
if args.to == 'obo':
write_obo(g,mo,args)
else:
write_tsv(lexmap,g,mo,args)
if args.unmapped:
udf = lexmap.unmapped_dataframe(g)
udf.to_csv(args.unmapped, sep="\t", index=False)
def main():
"""
Wrapper for OGR
"""
parser = argparse.ArgumentParser(
description='Wrapper for ontobio lexical mapping'
"""
...
""",
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('-o',
'--outfile',
type=str,
required=False,
help='Path to output file')
parser.add_argument('-t',
'--to',
type=str,
required=False,
default='tsv',
help='Output to (tree, dot, ...)')
parser.add_argument('-l',
'--labels',
type=str,
help='If set, then include node labels in results')
parser.add_argument(
'-P',
'--prefix',
type=str,
required=False,
help='Prefix to constrain traversal on, e.g. PATO, ENVO')
parser.add_argument('-v',
'--verbosity',
default=0,
action='count',
help='Increase output verbosity')
parser.add_argument('ontologies', nargs='*')
args = parser.parse_args()
if args.verbosity >= 2:
logging.basicConfig(level=logging.DEBUG)
elif args.verbosity == 1:
logging.basicConfig(level=logging.INFO)
else:
logging.basicConfig(level=logging.WARNING)
logging.info("Welcome!")
factory = OntologyFactory()
onts = [factory.create(h) for h in args.ontologies]
lexmap = LexicalMapEngine()
if len(onts) == 0:
raise ValueException("must pass one or more ontologies")
else:
for ont in onts:
lexmap.index_ontology(ont)
mo = Ontology()
mo.merge(onts)
g = lexmap.get_xref_graph()
if args.to == 'obo':
write_obo(g, mo, args)
else:
write_tsv(g, mo, args)