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From Danilo Tomasoni <tomas...@cosbi.eu>
Subject SynonimGraphFilter expands wrong synonims
Date Wed, 05 Sep 2018 10:19:58 GMT
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

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

and two documents

{"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."}

Body has the type "text_en" configured in this way

<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>

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

(body:"Cytosolic 5'-nucleotidase II"  OR body:"EC 3.1.3.5")

both documents are returned.

Surprisingly, if I run the query

(body:"Cytosolic 5'-nucleotidase II")

the second one is not returned.

If I set debugQuery=true I see that the second line is expanded

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

instead of the first

P49902,Cytosolic purine 5'-nucleotidase,EC 3.1.3.5,Cytosolic 5'-nucleotidase II

The parsed query (given by debugquery) is

"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))

If I remove the second line, no synonym is expanded

     "parsedquery":"PhraseQuery(body_unnamed:\"cytosol 5 nucleotidas ii\")",

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.

Thank you

-- 
Danilo Tomasoni
COSBI

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