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From Danilo Tomasoni <tomas...@cosbi.eu>
Subject Re: SynonimGraphFilter expands wrong synonims
Date Wed, 05 Sep 2018 13:58:28 GMT
Hi Andrea,

thank you for your answer.

About the second question: The standardTokenizer should be applied also 
to the phrase query, so the ' and - symbols should be removed even 
there, and this should allow a match in the synonim file isn't it?

With an example:


in phrase query:

"Cytosolic 5'-nucleotidase II" -> standardTokenizer -> Cytosolic, 5, 
nucleotidase, II


in synonym parsing:

...,Cytosolic 5'-nucleotidase II,... -> standardTokenizer -> Cytosolic, 
5, nucleotidase, II


So the two graphs should match.. or I'm wrong?
Thank you
Danilo

ody:On 05/09/2018 13:23, Andrea Gazzarini wrote:
> Hi Danilo,
> let's see if this can help you (I'm sorry for the poor debugging, I'm 
> reading & writing from my mobile): the first issue should have 
> something to do with synonym overlapping and since I'm very curious 
> about what it is happening, I will be more precise when I will be in 
> front of a laptop.
>
> The second: I guess the main problem is the StandardTokenizer, which 
> removes the ' and - symbols. That should be the reason why you don't 
> have any synonym detection. You should replace it with a 
> WhitespaceTokenizer but, be aware that if you do that, the apostrophe 
> in the document ( ′ ) is not the same symbol ( ' ) you've used in the 
> query and in the synonyms file, so you need to replace it somewhere 
> (in the document and/or in the query) otherwise you won't have any match.
>
> HTH
> Gazza
>
> On 05/09/2018 12:19, Danilo Tomasoni wrote:
>> 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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