PPLRE Closed Curation Issue

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A PPLRE Closed Curation Issue is a PPLRE curation issue that is a closed curation issue.

CI070228.2

  • OpenedBy: Gabor Melli.
  • Version: v1.3
  • Description: In Sent=600.0 the protein name is very very long” pyrroloquinoline quinone (PQQ ) -dependent polyvinyl alcohol (PVA ) dehydrogenase". Nancy however confirmed that this indeed is the full name.
  • Example:” A novel enzyme, pyrroloquinoline quinone (PQQ ) -dependent polyvinyl alcohol (PVA ) dehydrogenase, was found in and partially purified from the membrane fraction of a PVA-degrading symbiont, Pseudomonas sp. strain VM15C ."
  • Action: No action required.

CI070228.3

  • OpenedBy: Gabor Melli, Homira Mojtabaei, Zhongmin Shi.
  • Description: There is a bug in tuples #17 and #18 (in OPL.Test). The relations S.Marcescens, HasE or HasD, outer membrane) are incorrectly associated to sentence 6171.2 (neither protein is in the sentence). In fact the correct sentence is 6171.4 and the location is inner membrance.
  • Example:
    • <sent=2> "HasA secretion was reconstituted in Escherichia coli, and we show here that like many proteins lacking a signal peptide, HasA has a C-terminal targeting sequence and is secreted by a specific ATP binding cassette (ABC ) transporter consisting of three proteins, one inner membrane protein with a conserved ATP binding domain, called the ABC ; a second inner membrane protein ; and a third, outer membrane component ."
    • <sent=4> "It consists of the two S. marcescens inner membrane-specific components, HasD and HasE, associated with an outer membrane component coming from another bacterial ABC transporter, such as the E. coli TolC protein, the outer membrane component of the hemolysin transporter, or the Erwinia chrysanthemi PrtF protein, the outer membrane component of the protease transporter.
  • Action: In v1.3.1 changed sentence to 6171.4 and changed location to inner membrane.

CI070304.1a

  • OpenedBy: Gabor Melli.
  • Version: v1.3
  • Description: PPLRE Corpus 200.a does not contain two relations that are not curated (PS1->secreted & PS2->secreted).
  • Example:
    • <sent=0> Two proteins, PS1 and PS2, were detected in the culture medium of Corynebacterium glutamicum and are the major proteins secreted by this bacterium.
  • Plan:
    • Gabor to review comments in curation form before sending for review.

CI070304.1b

  • OpenedBy: Gabor Melli.
  • Version: v1.3
  • Description: PPLRE Corpus 200.a.5-6 the curated selection of PS-1 ⇒ periplasmic seems odd. Nancy confirmed that this is not a positive case because the 'protein' is a "protein band".
  • Example:
    • <sent=5> The major protein band, of lower M(r), was detected in the periplasmic fraction.
    • <sent=6> It had the same M(r) as the PS1 protein band detected in the supernatant of C. glutamicum cultures and presumably corresponds to the mature form of PS1.
    • Action: In v1.3.1 changed label to -1 (from +1)

CI070316.1

  • OpenedBy: Gabor Melli.
  • Version: v1.3
  • Description: PSID=1671.6 is in a negative test case even though there is no location.
  • Example(s): "To further localize IalB, B. bacilliformis inner and outer membranes were fractionated by sucrose density gradient centrifugation and identified by appearance, buoyant density, and cytochrome b content.
  • Action: v1.3.1 deletes tuple 592

CI070318.1

  • OpenedBy: Gabor Melli.
  • Version: v1.3
  • Description: Tuple 290 (PSID=7070) ranges over five sentences. The organism though can be found closer though to the protein and location.
  • Example(s): <sent> The mannose-sensitive hemagglutinin (MSHA) of the Vibrio cholerae O1 El Tor biotype is a member of the family of type 4 pili. </sent> <sent> Type 4 pili are found on the surface of a variety of gram-negative bacteria and have demonstrated importance as host colonization factors, bacteriophage receptors, and mediators of DNA transfer. </sent> <sent> The gene locus required for the assembly and secretion of the MSHA pilus has been localized to a 16.7-kb region of the V. cholerae chromosome. </sent> <sent> Sixteen genes required for hemagglutination, including five that encode prepilin or prepilin-like proteins, have been identified. </sent> <sent> Examination of MSHA-specific cDNAs has localized two promoters that drive expression of these genes. </sent> <sent> This evidence indicates that the MSHA gene locus is transcriptionally organized into two operons, one encoding the secretory components and the other encoding the structural subunits, an arrangement unique among previously characterized type 4 pilus loci. </sent>"
  • Action: In v1.3.1 changed the sentence for the organism to sentence=2 (from sentence=0).

CI070324.1

  • OpenedBy: Gabor Melli.
  • Version: v1.3
  • Description: Several curated records in the MS Access databases (at least in v1.2) are not in the v1.3 data. This discovery resulted from my search for passages that the curators deemed to containt an OPL relation but not based on direct experimental evidence. Many of them are contain the either the word "indirect" or "weak" in the "Comments" field.
  • Example(s):
    • Examples where Geoff marked a passage as MaybeValidPrediction=TRUE and ValidPrediction=FALSE and a Comment=~/indirect|weak/
      • PSID=2065 (under database LocalizationID=464)
      • PSID 2736 (under database LocalizationID=501)
      • There may be others
  • Action: Too much work to figure these out. Do nothing.

CI0700403.1

  • OpenedBy: Gabor Melli.
  • Version: v1.3
  • Description: The relation case in TupleID=227 (PSID=1551) spans two sentences when in fact the ralation exists in the single sentence.
  • Example(s):
    • <sent=0> Legionella pneumophila, the etiologic agent of Legionnaires' disease, contains a single, monopolar flagellum which is composed of one major subunit, the FlaA protein.
    • <sent=1> To evaluate the role of the flagellum in the pathogenesis and ecology of Legionella, the flaA gene of L. pneumophila Corby was mutagenized by introduction of a kanamycin resistance cassette.
  • Action: In v1.3.1 changed the sentence associated with the location to be sent=0 (from sent=1).

CI0700418.2

  • OpenedBy: Zhongmin Shi.
  • Version: v1.3
  • Description: In tuple=#1103 the PSID=7970.5 should be changed to PSID=7970.1
  • Example:
    • <sent=2> Incubation of CHO cells with intact B. pertussis led to formation of intracellular cAMP at levels comparable to those produced in CHO cells by equivalent activities of isolated AC toxin.
    • <sent=5> Transmission electron micrographs revealed that B. pertussis, within the time course of cAMP induction, invaded CHO cells.
  • Action: In v1.3.1 changed the sentenceId on all three entities to sent=1 (from sent=5)

CI0700418.3

  • OpenedBy: Zhongmin Shi.
  • Version: v1.3
  • Description: In tuple=#1104 the PSID=7970.6 should be changed to PSID=7970.2
  • Example:
    • <sent=2> Sera of pertussis patients completely blocked cAMP accumulation induced by the whole bacteria without having a major effect on either bacterial adherence or cAMP production by the AC toxin.
    • <sent=6> We suggest that cAMP induction by B. pertussis is caused by the entry of the whole bacteria into CHO cells rather than by delivery of AC toxin during bacterial adherence.
  • Action: In v1.3.1 changed the sentenceId on all three entities to sent=2 (from sent=6)

CI0700418.4

  • OpenedBy: Zhongmin Shi.
  • Version: v1.3
  • Description: In tuple=#892(PSID=4690.3) is not in the reviewed sets. We may want to remove it.
  • Action: In v1.3.1 tuple=#892 is removed.

CI0700418.5

  • OpenedBy: Zhongmin Shi.
  • Version: v1.3
  • Description: In tuple=#1040 (PSID=6630.0) the case <OmpA, outer membrane, Escherichia coli> is mislabeled as negative.
  • Example: "Heterologous protein secretion was studied in the gram-positive bacteria Bacillus subtilis and Staphylococcus carnosus by using the Escherichia coli outer membrane protein OmpA as a model protein."
  • Action: In v1.3.1 tuple=#1040 is changed to +1 (from -1).

CI0700429.1

  • OpenedBy: Gabor Melli and Nancy Yu.
  • Version: v1.3
  • Description: In tuple=#391 (PSID=14260.0) is mislabeled. It currently has a positive label when it should be a negative label. The entity marked as a protein in the sentence (Pyoluteorin) is not a protein.
  • Example: "Pyoluteorin is a chlorinated polyketide antibiotic secreted by the rhizosphere bacterium Pseudomonas fluorescens Pf-5."
  • Action: In v1.3.1 tuple=#391 is changed to -1 (from +1).
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