A PPLRE Curation Issues is a curation issue for a PPLRE Project.

Context:
- The issures relate to version PPLRE Curated Data v1.3.
- These are candidates for resolution when creating the next version PPLRE Curated Data v1.4. A version which will is planned for after the next round of curation.
- It can be a PPLRE Closed Curation Issue.
See: Annotation Guideline.

Items

CI070228.1

OpenedBy: Gabor Melli.
Version: v1.3
Description: Sent=3131.0 contains two instances of the same protein. It is an example where the protein name is mentioned and then the abbreviated name immediately followin in parentheses.
Example: "The temperature-sensitive hemagglutinin (Tsh ) is an autotransporter protein secreted by avian-pathogenic Escherichia coli strains that colonize the respiratory tract and lead to airsacculitis, pericarditis, and colisepticemia ."
Plan: Add a new record in v1.4; similar to tupleid=199 but with the long name "temperature-sensitive hemagglutinin"

CI070304.1b

OpenedBy: Gabor Melli.
Description: In PSID=200.0 “<sent> Two proteins, PS1 and PS2, were detected in the culture medium of Corynebacterium glutamicum and are the major proteins secreted by this bacterium. </sent>"
Suggestion: Add two positive cases in v1.4.

CI070318.2

OpenedBy: Gabor Melli.
Version: v1.3
Description: Only one of two locations is curated PSID=491 (i.e. TUPLE_IDs 173, 174, 175, and 176). Specifically the cytoplasmic membrane location is curated but there is no record for the outer membrane locations.
Example(s): <491.a.2> In this study, Escherichia coli TonB was found to be distributed in sucrose density gradients approximately equally between the cytoplasmic membrane and the outer membrane fractions, while two proteins with which it is known to interact, ExbB and ExbD, as well as the NADH oxidase activity characteristic of the cytoplasmic membrane, were localized in the cytoplasmic membrane fraction.
Suggestion: Add two positive cases (w/ outer membrane) in v1.4.

CI0700418.5

OpenedBy: Zhongmin Shi.
Version: v1.3
Description: In tuple=#1040 (PSID=6630.0) there are two negative examples that can be added. The positive example is already present.

coli>. Some examples in the train set also support this:

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."

Suggestion: Add two negative cases to v1.4.

CI0700418.1

OpenedBy: Gabor Melli.
Version: v1.3
Description: In PSID=1000.0 the organism name "Alcaligenes eutrophus" should be accepted (not just the official "Ralstonia eutropha") because it resolves to the correct NCBI TaxId=106590.
Example(s): "Ralstonia eutropha (formerly Alcaligenes eutrophus) TF93 is pleiotropically ..."
Suggestion: Add a record to v1.4.

CI0700516.1

OpenedBy: Gabor Melli.
Version: v1.3.1
Description: Issue in the train data

111 PscF 243 7 P. aeruginosa 243 7 secretion 243 7 1 GO0005576 Thus, PscE and PscG prevent PscF from polymerizing prematurely in the P. aeruginosa cytoplasm and keep it in a secretion prone conformation, strategies which may be shared by other pathogens that employ the T3S system for infection. Two

CI0700516.2

OpenedBy: Gabor Melli.
Version: v1.3.1
Description: Issue in the train data

62 cellobiase 6305 8 F. succinogenes 6305 8 extracellular membrane 6305 8 1 GO0005576 Thus, we have documented a method for isolation of OM from F. succinogenes, identified the OM origin of the extracellular membrane vesicles, and located glycanases and cellobiase in membrane and glycogen fractions.

CI0700516.3

OpenedBy: Gabor Melli.
Version: v1.3.1
Description: Issue in the train data

4 AdnA 2298 0 Pseudomonas fluorescens 2298 0 flagellar 2298 0 1 GO0009288 AdnA is a transcription factor in Pseudomonas fluorescens that affects flagellar synthesis, biofilm formation, and sand adhesion.

CI0700516.4

OpenedBy: Gabor Melli.
Version: v1.3.1
Description: Issue in the train data

126 lipase 499 1 Pseudomonas aeruginosa TE3285 499 0 extracellular 499 0 1 287 GO0005576 An extracellular lipase secreted by Pseudomonas aeruginosa TE3285 was purified. A genomic library of this strain was constructed in lambda EMBL3, and a DNA fragment 2.7 kb long containing the lipase gene, lipA, was isolated with an oligonucleotide probe synthesized on the basis of the partial amino acid sequence of a purified preparation of the enzyme.

PPLRE Curation Issues