Danilo Tomasoni created SOLR-12731:
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Summary: SynonimGraphFilter expands wrong synonims
Key: SOLR-12731
URL: https://issues.apache.org/jira/browse/SOLR-12731
Project: Solr
Issue Type: Bug
Security Level: Public (Default Security Level. Issues are Public)
Components: search
Affects Versions: 7.3.1
Environment: Ubuntu 16.04.5 LTS
Reporter: Danilo Tomasoni
Hello to all I have an issue related to synonimgraphfilter expanding the wrong
synonims for a phrase-term at query time.
I have a dictionary with the following lines
{code:java}
P49902,Cytosolic purine 5'-nucleotidase,EC 3.1.3.5,Cytosolic 5'-nucleotidase II
A8K9N1,Glucosidase\, beta\, acid 3,Cytosolic,Glucosidase\, beta\, acid
3,Cytosolic\, isoform CRA_b,cDNA FLJ78196\, highly similar to Homo sapiens
glucosidase\, beta\, acid 3,cytosolic,GBA3\, mRNA,cDNA\, FLJ93688\, Homo
sapiens glucosidase\, beta\, acid 3,cytosolic,GBA3\, mRNA
{code}
and two documents
{code:java}
{"body": "8. The method of claim 6 wherein said method inhibits at least one
5′-nucleotidase chosen from cytosolic 5′-nucleotidase II (cN-II), cytosolic
5′-nucleotidase IA (cN-IA), cytosolic 5′-nucleotidase IB (cN-IB), cytosolic
5′-nucleotidase IMA (cN-IIIA), cytosolic 5′-nucleotidase NIB (cN-IIIB),
ecto-5′-nucleotidase (eN, CD73), cytosolic 5′(3′)-deoxynucleotidase (cdN) and
mitochondrial 5′(3′)-deoxynucleotidase (mdN)."}
{"body": "Trichomonosis caused by the flagellate protozoan Trichomonas
vaginalis represents the most prevalent nonviral sexually transmitted disease
worldwide (WHO-DRHR 2012). In women, the symptoms are cyclic and often worsen
around the menstruation period. In men, trichomonosis is largely asymptomatic
and these men are considered to be carriers of T. vaginalis (Petrin et al.
1998). This infection has been associated with birth outcomes (Klebanoff et al.
2001), infertility (Grodstein et al. 1993), cervical and prostate cancer
(Viikki et al. 2000, Sutcliffe et al. 2012) and pelvic inflammatory disease
(Cherpes et al. 2006). Importantly, T. vaginalis is a co-factor in human
immunodeficiency virus transmission and acquisition (Sorvillo et al. 2001, Van
Der Pol et al. 2008). Therefore, it is important to study the host-parasite
relationship to understand T. vaginalis infection and pathogenesis.
Colonisation of the mucosa by T. vaginalis is a complex multi-step process that
involves distinct mechanisms (Alderete et al. 2004). The parasite interacts
with mucin (Lehker & Sweeney 1999), adheres to vaginal epithelial cells (VECs)
in a process mediated by adhesion proteins (AP120, AP65, AP51, AP33 and AP23)
and undergoes dramatic morphological changes from a pyriform to an amoeboid
form (Engbring & Alderete 1998, Kucknoor et al. 2005, Moreno-Brito et al.
2005). After adhesion to VECs, the synthesis and gene expression of adhesins
are increased (Kucknoor et al. 2005). These mechanisms must be tightly
regulated and iron plays a pivotal role in this regulation. Iron is an
essential element for all living organisms, from the most primitive to the most
complex, as a component of haeme, iron-sulphur clusters and a variety of
proteins. Iron is known to contribute to biological functions such as DNA and
RNA synthesis, oxygen transport and metabolic reactions. T. vaginalis has
developed multiple iron uptake systems such as receptors for hololactoferrin,
haemoglobin (HB), haemin (HM) and haeme binding as well as adhesins to
erythrocytes and epithelial cells (Moreno-Brito et al. 2005, Ardalan et al.
2009). Iron plays a crucial role in the pathogenesis of trichomonosis by
increasing cytoadherence and modulating resistance to complement lyses,
ligation to the extracellular matrix and the expression of proteases
(Figueroa-Angulo et al. 2012). In agreement with this role, the symptoms of
trichomonosis worsen after menstruation. In addition, iron also influences
nucleotide hydrolysis in T. vaginalis (Tasca et al. 2005, de Jesus et al.
2006). The extracellular concentrations of ATP and adenosine can markedly
increase under several conditions such as inflammation and hypoxia as well as
in the presence of pathogens (Robson et al. 2006, Sansom 2012). In the
extracellular medium, these nucleotides can act as immunomodulators by
triggering immunological effects. Extracellular ATP acts as a proinflammatory
immune-mediator by triggering multiple immunological effects on cell types such
as neutrophils, macrophages, dendritic cells and lymphocytes (Bours et al.
2006). In this sense, ATP and adenosine concentrations in the extracellular
compartment are controlled by ectoenzymes, including those of the nucleoside
triphosphate diphosphohydrolase (NTPDase) (EC: 3.1.4.1) family, which hydrolyze
tri and diphosphates and ecto-5’-nucleotidase (EC: 3.1.3.5), which hydrolyses
monophosphates (Zimmermann 2001). Considering that de novo nucleotide synthesis
is absent in T. vaginalis (Heyworth et al. 1982, 1984), this enzyme cascade is
important as a source of the precursor adenosine for purine synthesis in the
parasite (Munagala & Wang 2003). Extracellular nucleotide metabolism has been
characterised in several parasite species such as Toxoplasma gondii,
Schistosoma mansoni, Leishmania spp, Trypanosoma cruzi, Acanthamoeba, Entamoeba
histolytica, Giardia lamblia and fungi, Saccharomyces cerevisiae, Cryptococcus
neoformans, Candida parapsilosis and Candida albicans (Sansom 2012). In T.
vaginalis , NTPDase and ecto-5’-nucleotidase activities have been characterised
and they are involved in host-parasite interactions by controlling ATP and
adenosine levels (Matos et al. 2001, d, de Jesus et al. 2002, Tasca et al.
2003). Considering that (i) iron plays a crucial role in the pathogenesis of
trichomonosis, (ii) ATP exerts a proinflammatory effect in inflammation, (iii)
adenosine is important to T. vaginalis growth and acts as an antiinflammatory
factor (Frasson et al. 2012) and (iv) ectonucleotidases modulate the nucleotide
levels at infection sites (such as those observed in trichomonosis), the aim of
this study was to investigate the effect of iron on the extracellular
nucleotide hydrolysis and gene expression of T . vaginalis."}
{code}
Body has the type "text_en" configured in this way
{code:java}
<fieldType name="text_en" class="solr.TextField" positionIncrementGap="100">
<analyzer type="index">
<tokenizer class="solr.StandardTokenizerFactory"/>
<filter class="solr.StopFilterFactory"
ignoreCase="true"
words="lang/stopwords_en.txt"
/>
<filter class="solr.LowerCaseFilterFactory"/>
<filter class="solr.EnglishPossessiveFilterFactory"/>
<filter class="solr.KeywordMarkerFilterFactory"
protected="protwords.txt"/>
<filter class="solr.PorterStemFilterFactory"/>
</analyzer>
<analyzer type="query">
<tokenizer class="solr.StandardTokenizerFactory"/>
<filter class="solr.StopFilterFactory"
ignoreCase="true"
words="lang/stopwords_en.txt"
/>
<filter class="solr.SynonymGraphFilterFactory" synonyms="synonyms.txt"
ignoreCase="true" expand="true"/>
<filter class="solr.LowerCaseFilterFactory"/>
<filter class="solr.EnglishPossessiveFilterFactory"/>
<filter class="solr.KeywordMarkerFilterFactory"
protected="protwords.txt"/>
<filter class="solr.PorterStemFilterFactory"/>
</analyzer>
</fieldType>
{code}
the two dictionary lines are in the file "synonyms.txt".
If in a solr instance configured this way with those documents and I run the
following query
{code:java}
(body:"Cytosolic 5'-nucleotidase II" OR body:"EC 3.1.3.5")
{code}
both documents are returned.
Surprisingly, if I run the query
{code:java}
(body:"Cytosolic 5'-nucleotidase II")
{code}
the second one is not returned.
If I set debugQuery=true I see that the second line is expanded
{code:java}
A8K9N1,Glucosidase\, beta\, acid 3,Cytosolic,Glucosidase\, beta\, acid
3,Cytosolic\, isoform CRA_b,cDNA FLJ78196\, highly similar to Homo sapiens
glucosidase\, beta\, acid 3,cytosolic,GBA3\, mRNA,cDNA\, FLJ93688\, Homo
sapiens glucosidase\, beta\, acid 3,cytosolic,GBA3\, mRNA
{code}
instead of the first
{code:java}
P49902,Cytosolic purine 5'-nucleotidase,EC 3.1.3.5,Cytosolic 5'-nucleotidase II
{code}
The parsed query (given by debugquery) is
{code:java}
"parsedquery":"SpanNearQuery(spanNear([spanOr([body:a8k9n1,
spanNear([body:glucosidase,, body:beta,, body:acid, body:3], 0, true),
spanNear([body:cytosolic,, body:isoform, body:cra_b], 0, true),
spanNear([body:cdna, body:flj78196,, body:highli, body:similar, body:to,
body:homo, body:sapien, body:glucosidase,, body:beta,, body:acid, body:3], 0,
true), body:cytosol, spanNear([body:gba3,, body:mrna], 0, true),
spanNear([body:cdna,, body:flj93688,, body:homo, body:sapien,
body:glucosidase,, body:beta,, body:acid, body:3], 0, true), body:cytosol]),
body:5, body:nucleotidas, body:ii], 0, true))
{code}
If I remove the second line, no synonym is expanded
{code:java}
"parsedquery":"PhraseQuery(body_unnamed:\"cytosol 5 nucleotidas ii\")",
{code}
I think this is related to the word "cytosolic" that appears as a synonim for
the second line. If I remove cytosolic as a synonim from the second line, then
again no synonym is expanded.
Can you tell me why this happens? I thought that the first line should be
expanded since it has a multi-word synonym in it that match exactly the phrase
query.
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