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Resolving abbreviated bacterial names

Hi community,

I am working in the area of text mining and working with full-text articles. I encounter a number of bacterial names and their abbreviated forms also. But I have issues resolving the text for example

"M. chelonae is a rapidly growing mycobacterium."

So here I am able to detect the name M. Chelonae and now comes the issue. When I search NCBI taxonomy or LPSN I get no results.

Any pointers on how to resolve this are welcome.

microbiology python taxonomy
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updated by GenoMax GenoMax • written by Arindam • Arindam

2 answers

Updated answer:

$ esearch -db pubmed -query "chelonae"  | esummary | xtract -pattern DocumentSummary -element Title | grep  -Eo '\w+ chelonae '
Mycobacterium chelonae 
Mycobacterium chelonae 
Mycobacterium chelonae

Below was original answer but Mensur Dlakic 's comment led to version above.

Disclaimer: This is not a fool-proof way of getting this information and may not work for all cases.

Using Entrezdirect:

$ esearch -db pubmed -query " chelonae"  | esummary | xtract -pattern DocumentSummary -element Title  | head -5
Draft Genome Sequence of a **Mycobacterium chelonae** subsp. bovis Strain Isolated from a Baikal Seal (Pusa sibirica) in Captivity.
Disseminated Mycobacterium chelonae infection complicating rheumatoid arthritis: A case report and review of the literature.
A Rare Case of Osteomyelitis of an Ankle Caused by Mycobacterium chelonae.
Successful treatment of cutaneous Mycobacterium chelonae infection by switching from levofloxacin to sitafloxacin.
Infectious eccrine hidradenitis caused by Mycobacterium chelonae in a patient with sarcoidosis.
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written by GenoMax GenoMax

chelonae is a somewhat unique species name. Here is what I get with thermophilus:

esearch -db pubmed -query " thermophilus"  | esummary | xtract -pattern DocumentSummary -element Title  | head -5

Endogenous small intestinal microbiome determinants of transient colonisation efficiency by bacteria from fermented dairy products: a randomised controlled trial.
Safety and efficacy of a feed additive consisting of endo-1,4-β-d-mannanase produced by Thermothelomyces thermophilusDSM 33149 (Natupulse® TS/TS L) for chickens and turkeys for fattening, minor poultry species for fattening and ornamental birds (BASF SE).
Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism.
A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments.
Yogurt starter strains ameliorate intestinal barrier dysfunction via activating AMPK in Caco-2 cells.

Or leprae:

esearch -db pubmed -query " leprae" | esummary | xtract -pattern DocumentSummary -element Title | head -5

Association of the rs2111234, rs3135499, rs8057341 polymorphisms in the NOD2 gene with leprosy: A case-control study in the Norte de Santander, Colombia population.
Patterns and Trends of Tribal Leprosy: An Overview from a Tertiary Care Leprosy Clinic of Choto Nagpur Plateau of Eastern India.
Leprosy (Hansen's disease): An Update and Review.
Non-tuberculous mycobacteria infection presenting as a hepatic allograft abscess.
The Revision of Lichen Flora Around Maxwell Bay, King George Island, Maritime Antarctic.
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written by Mensur Dlakic Mensur Dlakic

This is better. Word after can be included to get strains etc. or use second example to get the Genus species.

$ esearch -db pubmed -query "thermophilus"  | esummary | xtract -pattern DocumentSummary -element Title | grep  -Eo '\w+ thermophilus \w+'
Streptococcus thermophilus during
Streptococcus thermophilus Strains
Streptococcus thermophilus and
Streptococcus thermophilus BT01
Streptococcus thermophilus XJ53
Streptococcus thermophilus VHProbi
Streptococcus thermophilus strains
Streptococcus thermophilus in
Thermus thermophilus HB27

$ esearch -db pubmed -query "leprae"  | esummary | xtract -pattern DocumentSummary -element Title | grep  -Eo '\w+ leprae '
Mycobacterium leprae 
Mycobacterium leprae 
Mycobacterium leprae 
Mycobacterium leprae
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written by GenoMax GenoMax

"M. chelonae is a rapidly growing mycobacterium."

You already have an answer, as M stands for Mycobacterium. There is no way to figure the abbreviations just on their own and without any context. In your case the context was in the remainder of the same sentence. Usually the full name is used first somewhere in the article, or at least the genus is mentioned. After that the genus is abbreviated - that would be the M. - and only the species name (chelonae) is spelled out in full.

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written by Mensur Dlakic Mensur Dlakic

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