189
In this chapter we used basic concepts of text mining to retrieve the relevant
articles on fungal siderophores related to human. We applied bioinformatics technique to determine the genes and protein targets involved in siderophore biosynthetic pathways of various fungal organisms. Four experts with extensive knowledge
in bioinformatics, physiology and pharmacology annotated the retrieved articles
with human-related diseases, drugs and their association with fungal siderophores.
Experts summarized the knowledge hidden within the retrieved articles and included
the bioinformatics validation. We believe that this chapter will benefit the researchers in the field of microbiology by summarizing the contents available in the
PubMed database.
12.2 Citation Retrieval
PubMed contains 12,679 articles related to siderophores (on 11 June 2019). Among
these, 4795 articles are related to humans. However, Boolean query (i.e., “fungal
siderophore” OR “fungal siderophores” AND human) retrieved only 10 articles for
fungal siderophores related to humans. We observed that 811 PubMed articles (out
of 4795) contain fungi or fungus in the title or abstract based on the Boolean query
(siderophore OR siderophores) AND (fungi OR fungus). We suspect that many of
these articles could be false positives with co-occurring terms, siderophore and fungi.
Our approach to retrieve relevant articles for the current chapter is simple. We
used E-Utilities from NCBI (National Center for Biotechnology Information) to
retrieve 4795 article IDs (PMID) related to siderophores and annotated with
‘Human’ in the Medical Subject Heading (MeSH) index. Our customized E-Utilities
query is https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&ter
m=(“siderophore” OR “siderophores”) AND humans[MeSH] &retmax = 20,000.
All the retrieved PubMed articles may not contain abstracts. We filtered 3603 articles with abstracts and retrieved 106 PubMed articles related to human and fungal
siderophores. We restricted the search to articles annotated with “Humans” and
“Fungi” in the MeSH index. Our customized E-Utilities query for this retrieval is
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=(“side
rophore” OR “siderophores”) AND humans[MeSH] AND fungi[MeSH] AND has
abstract[Text] &retmax = 20,000. Our approach avoided many false positives. Thus,
our approach obtained 10 times more PubMed articles when compared to the
Boolean query search in the PubMed database.
12.3 Organisms Annotation
PubMed articles are annotated with organisms in the MeSH index. Though the
retrieved articles are annotated with “Human”, it would be interesting to know all
the annotated organisms. We used the NCBI taxonomy to map the organisms and
12 A Summary on Up-To-Date Research on Fungal Siderophores on Disease…
In this chapter we used basic concepts of text mining to retrieve the relevant
articles on fungal siderophores related to human. We applied bioinformatics technique to determine the genes and protein targets involved in siderophore biosynthetic pathways of various fungal organisms. Four experts with extensive knowledge
in bioinformatics, physiology and pharmacology annotated the retrieved articles
with human-related diseases, drugs and their association with fungal siderophores.
Experts summarized the knowledge hidden within the retrieved articles and included
the bioinformatics validation. We believe that this chapter will benefit the researchers in the field of microbiology by summarizing the contents available in the
PubMed database.
12.2 Citation Retrieval
PubMed contains 12,679 articles related to siderophores (on 11 June 2019). Among
these, 4795 articles are related to humans. However, Boolean query (i.e., “fungal
siderophore” OR “fungal siderophores” AND human) retrieved only 10 articles for
fungal siderophores related to humans. We observed that 811 PubMed articles (out
of 4795) contain fungi or fungus in the title or abstract based on the Boolean query
(siderophore OR siderophores) AND (fungi OR fungus). We suspect that many of
these articles could be false positives with co-occurring terms, siderophore and fungi.
Our approach to retrieve relevant articles for the current chapter is simple. We
used E-Utilities from NCBI (National Center for Biotechnology Information) to
retrieve 4795 article IDs (PMID) related to siderophores and annotated with
‘Human’ in the Medical Subject Heading (MeSH) index. Our customized E-Utilities
query is https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&ter
m=(“siderophore” OR “siderophores”) AND humans[MeSH] &retmax = 20,000.
All the retrieved PubMed articles may not contain abstracts. We filtered 3603 articles with abstracts and retrieved 106 PubMed articles related to human and fungal
siderophores. We restricted the search to articles annotated with “Humans” and
“Fungi” in the MeSH index. Our customized E-Utilities query for this retrieval is
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=(“side
rophore” OR “siderophores”) AND humans[MeSH] AND fungi[MeSH] AND has
abstract[Text] &retmax = 20,000. Our approach avoided many false positives. Thus,
our approach obtained 10 times more PubMed articles when compared to the
Boolean query search in the PubMed database.
12.3 Organisms Annotation
PubMed articles are annotated with organisms in the MeSH index. Though the
retrieved articles are annotated with “Human”, it would be interesting to know all
the annotated organisms. We used the NCBI taxonomy to map the organisms and
12 A Summary on Up-To-Date Research on Fungal Siderophores on Disease…