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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