Bioscape Searching Techniques

A number of searching techniques are applied to find textual mentions of entities or concepts, particularly those where the nature of the searching is speculative, meaning that no predefined lists of search terms is used, but where certain characteristic patterns are sought after in the text.

Acronym Mentions

Mentions of acronym definition phrases involve the detection of sentences containing brackets ( and ), followed by a closer inspection of such sentences, applying regular expressions which look for one of the following patterns:

• An acronym-like term (upper-case letters, digits and hyphens) followed by a parenthesis phrase (a phrase in brackets)
• An acronym-like term in brackets, with the preceding text then being considered as the definition or explanation of the acronym

Upon identifying a possible acronym and explanation, a test is performed to attempt to match each initial (letter or number) with a word from the explanatory text. Here, although it is tempting to only take the first letter (or digit) from each word, other approaches may be necessary involving more sophisticated tokenisation. Consider the following examples:

PubMed #10639512

"In this study, we isolated and characterized the crucial gene at the breast cancer antiestrogen resistance 1 (BCAR1) locus."

breast cancer antiestrogen resistance 1	(	BCAR1	)
explanation		acronym
b, c, a, r, 1		BCAR1

• explanation initials correspond to acronym

PubMed #10484778

"Anhidrotic ectodermal dysplasia (EDA) is a human genetic disorder of impaired ectodermal appendage development."

Anhidrotic ectodermal dysplasia	(	EDA	)
explanation		acronym
a, e, d (not detectable in order)		EDA

• presumed explanation initials only correspond to acronym if reordered

PubMed #10484776

"We identified a glyoxylate reductase/hydroxypyruvate reductase (GRHPR) cDNA clone from a human liver expressed sequence tag (EST) library."

glyoxylate reductase/hydroxypyruvate reductase	(	GRHPR	)
explanation		acronym
g, r, h, p (within a word), r (requiring word analysis)		GRHPR

• presumed explanation initials only correspond if words are inspected more closely
• words must also isolated using a more sophisticated tokeniser than one which splits words using whitespace characters

PubMed #10226785

"The insulin receptor related receptor (IRR) is a heterotetrameric transmembrane receptor with intrinsic tyrosine kinase activity."

insulin receptor related receptor	(	IRR	)
explanation		acronym
i, r, r (should be ignored), r (requiring stop-word detection)		IRR

• presumed explanation initials only correspond if stop-words are discarded

"The IRR shares large homology with the insulin and the insulin-like growth factor-1 (IGF-I) receptor with regard to amino acid sequence and protein structure."

insulin-like growth factor-1	(	IGF-I	)
explanation		acronym
i, l (should be ignored), g, f, 1 (requiring stop-word detection, numeral conversion)		IGF-I

• presumed explanation initials only correspond if stop-words are discarded
• numerals must also be converted so that 1 and I can be matched

Chromosome and Maplocation Mentions

To be expanded...

PubMed #10684944

"mouse chromosome 17 and to human chromosome 16p13.3"

PubMed #10639512

"chromosome 16q23.1"

PubMed #10484772

"chromosome Xp11.2"

Synonym Definitions

PubMed #10880513

"Our previous studies have shown that activation of a related adhesion focal tyrosine kinase (RAFTK) (also known as Pyk2) is required for dexamethasone (Dex)-induced apoptosis in multiple myeloma (MM) cells and that human interleukin-6 (IL-6), a known growth and survival factor for MM cells, blocks both RAFTK activation and apoptosis induced by Dex."

related adhesion focal tyrosine kinase	(	RAFTK	) (	also known as		Pyk2	)
suggestion		suggestion		synonym correspondence		suggestion

PubMed #10910894

"Liver-expressed chemokine (LEC) is an unusually large CC chemokine, which is also known as LMC, HCC-4, NCC-4, and CCL16."

(	LEC	) is an unusually large CC chemokine, which is	also known as		LMC	,	HCC-4	,	NCC-4	, and	CCL16
	suggestion		synonym correspondence		suggestion		suggestion		suggestion		suggestion
	CCL16 (#6360)				CCL16 (#6360)		CCL16 (#6360) RBMS1 (#5937)		CCL16 (#6360)		CCL16 (#6360)

PubMed #11137999

"Here we report the identification of a new transmembrane serine protease (TMPRSS3; also known as ECHOS1) expressed in many tissues, including fetal cochlea, which is mutated in the families used to describe both the DFNB10 and DFNB8 loci."

TMPRSS3	;	also known as		ECHOS1
suggestion		synonym correspondence		suggestion
TMPRSS3 (#64699) TMPRSS4 (#56649)				TMPRSS3 (#64699)

Bioentity Inference

Sometimes, it can be inferred which kind of bioentity is being written about in the text.

PubMed #9624006

"These mice also show increased susceptibility to tumorigenesis either following carcinogen treatment or when also deficient in Ink4a."

deficient in		Ink4a
type-specific term		suggestion
reference to protein		CDKN2A (#1029)

• "deficient in" should force the interpretation of the bioentity as a protein

PubMed #8062391

"A novel positive cofactor (PC4) purified from the human USA fraction effected a marked enhancement (up to 85-fold) of GAL4-AH-dependent transcription in conjunction with TFIID and other general factors."

in conjunction with	TFIID	and other general	factors
	suggestion		type-specific term
	TBP (#6908)		reference to proteins

• syntactic analysis connecting the suggestion with "factors" should force the interpretation of the bioentity as a protein

PubMed #7663508

"The fat mutation maps to mouse chromosome 8, very close to the gene for carboxypeptidase E (Cpe), which encodes an enzyme (CPE) that processes prohormone intermediates such as proinsulin."

very close to	the gene for		carboxypeptidase E	(	Cpe	), which encodes an	enzyme	(	CPE	)
	type-specific term		suggestion		suggestion		type-specific term		suggestion
	reference to gene for protein		CPE (#1363)		CPE (#1363)		reference to protein		CPE (#1363)

• type-specific terms should cause suggestions to be interpreted as proteins, albeit with an implied gene reference
• note that "mouse chromosome 8" should affect any chromosome-related techniques

However, elsewhere in this document, text surrounding suggestions may cause other interpretations:

"Hyperproinsulinaemia in obese fat/fat mice associated with a carboxypeptidase E mutation which reduces enzyme activity."

associated with a	carboxypeptidase E		mutation
	suggestion		type-specific term
	CPE (#1363)		implied reference to gene

• "mutation" should cause the suggestion to be interpreted as a gene

PubMed #2674130

"A new family of ras-related proteins, designated rac (ras-related C3 botulinum toxin substrate) has been identified. rac1 and rac2 cDNA clones were isolated from a differentiated HL-60 library and encode proteins that are 92% homologous and share 58% and 26-30% amino acid homology with human rhos and ras, respectively."

A new	family	of ras-related	proteins	, designated	rac	(	ras-related C3 botulinum toxin substrate	)
	type-specific term		type-specific term		suggestion		acronym explanation (not detected)
	reference to protein family		reference to proteins		AKT1 (#207)

• syntactic analysis should connect the type-specific term to the suggestion and cause the suggestion to be interpreted as a protein family