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LitCovid Dataset

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Guoqian Jiang edited this page Apr 8, 2020 · 4 revisions

Total Instance Counts by Data Types

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX fhir: <http://hl7.org/fhir/>
PREFIX pmc: <https://www.ncbi.nlm.nih.gov/pmc/articles#>
select distinct ?pmc_type  (count(?pmc_type) as ?count) where { 
    ?pmc pmc:annotations ?annotations .
    ?annotations pmc:infons ?pmc_infons .
    ?pmc_infons pmc:identifier ?pmc_identifier .
    ?pmc_infons pmc:type ?pmc_type .
    ?annotations pmc:text ?text .    
    
} group by ?pmc_type  order by DESC(?count)


?pmc_type	?count
Species	34945
Disease	29106
Chemical	4718
Gene	4382
CellLine	460
Mutation	117

Total Document Counts

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX fhir: <http://hl7.org/fhir/>
PREFIX pmc: <https://www.ncbi.nlm.nih.gov/pmc/articles#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
select distinct (count(?pmc) as ?count) where { 
    ?pmc dc:source ?source   
} 

"3062"^^xsd:integer

Top Disease Instances

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX fhir: <http://hl7.org/fhir/>
PREFIX pmc: <https://www.ncbi.nlm.nih.gov/pmc/articles#>
select distinct ?pmc_type ?pmc_identifier ?text (count(?text) as ?count) where { 
    ?pmc pmc:annotations ?annotations .
    ?annotations pmc:infons ?pmc_infons .
    ?pmc_infons pmc:identifier ?pmc_identifier .
    ?pmc_infons pmc:type ?pmc_type .
    ?annotations pmc:text ?text .
    FILTER (?pmc_type='Disease').
    
    
} group by ?pmc_type ?pmc_identifier ?text order by DESC(?count)

?pmc_type	?pmc_identifier	?text	?count
Disease	MESH:C000657245	COVID-19	5565
Disease	MESH:D007239	infection	1929
Disease	MESH:D007239	infected	1542
Disease	MESH:D011014	pneumonia	1181
Disease	MESH:D005334	fever	705
Disease	MESH:D045169	SARS	691
Disease	MESH:D003643	mortality	519
Disease	MESH:D007239	infections	518
Disease	MESH:D003643	deaths	511
Disease	MESH:D003643	death	412
Disease	MESH:D018352	MERS	406
Disease	MESH:D012128	ARDS	385
Disease	MESH:D003371	cough	320
Disease	MESH:D016638	critically ill	304
Disease	MESH:C000657245	coronavirus disease 2019	269
Disease	MESH:C000657245	"2019-nCoV infection"	264
Disease	MESH:C000657245	novel coronavirus pneumonia	241
Disease	MESH:C000657245	SARS-CoV-2 infection	238
Disease	MESH:D001007	anxiety	236
Disease	MESH:D003141	infectious diseases	212
Disease	MESH:D012128	acute respiratory distress syndrome	210
Disease	MESH:D003141	infectious disease	202
Disease	MESH:D015047	zoonotic	200
Disease	MESH:D045169	severe acute respiratory syndrome	173
Disease	MESH:D003920	diabetes	171
Disease	MESH:D012131	respiratory failure	156
Disease	MESH:D009369	cancer	144
Disease	MESH:D011014	Pneumonia	141
Disease	MESH:D005221	fatigue	127
Disease	MESH:D000079225	stress	125
Disease	MESH:D007239	Infection	121
Disease	MESH:D003643	died	120
Disease	MESH:D006973	hypertension	120
Disease	MESH:C000657245	Covid-19	115
Disease	MESH:D000275	depression	114
Disease	MESH:C000657245	Coronavirus Disease 2019	112
Disease	MESH:D004417	dyspnea	112
Disease	MESH:D012120	acute respiratory syndrome	112
Disease	MESH:C000657245	COVID-19 pneumonia	110
Disease	MESH:D007249	inflammation	109
Disease	MESH:D012818	respiratory symptoms	109
Disease	MESH:D001102	viral infection	101
Disease	MESH:C000657245	NCP	100
Disease	MESH:D018352	Middle East respiratory syndrome	95
Disease	MESH:D012140	respiratory disease	92
Disease	MESH:D012141	respiratory infection	90
Disease	MESH:C000657245	novel coronavirus-infected pneumonia	89
Disease	MESH:D005334	Fever	89
Disease	MESH:D003967	diarrhea	83
Disease	MESH:D018805	sepsis	80

Top Species Instances

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX fhir: <http://hl7.org/fhir/>
PREFIX pmc: <https://www.ncbi.nlm.nih.gov/pmc/articles#>
select distinct ?pmc_type ?pmc_identifier ?text (count(?text) as ?count) where { 
    ?pmc pmc:annotations ?annotations .
    ?annotations pmc:infons ?pmc_infons .
    ?pmc_infons pmc:identifier ?pmc_identifier .
    ?pmc_infons pmc:type ?pmc_type .
    ?annotations pmc:text ?text .
    FILTER (?pmc_type='Species').
    
    
} group by ?pmc_type ?pmc_identifier ?text order by DESC(?count)

?pmc_type	?pmc_identifier	?text	?count
Species	"9606"	patients	6300
Species	"2697049"	"2019-nCoV"	3084
Species	"2697049"	SARS-CoV-2	2649
Species	"9606"	human	1896
Species	"694009"	SARS-CoV	1684
Species	"9606"	patient	1441
Species	"2697049"	novel coronavirus	898
Species	"1335626"	MERS-CoV	865
Species	"9606"	people	841
Species	"2501931"	coronavirus	790
Species	"2697049"	"2019 novel coronavirus"	643
Species	"2501931"	coronaviruses	592
Species	"9606"	humans	469
Species	"2501931"	CoV	434
Species	"2501931"	CoVs	343
Species	"9606"	children	331
Species	"11118"	coronavirus	311
Species	"9606"	Patients	308
Species	"9606"	Patient	267
Species	"9606"	persons	254
Species	"2697049"	new coronavirus	240
Species	"12814"	respiratory	237
Species	"9606"	women	185
Species	"114727"	H1N1	176
Species	"9606"	People	171
Species	"2501931"	Coronavirus	168
Species	"694009"	SARS coronavirus	166
Species	"694009"	severe acute respiratory syndrome coronavirus	158
Species	"2697049"	Novel Coronavirus	152
Species	"2501931"	HCoV	146
Species	"9606"	Human	137
Species	"2501931"	Coronaviruses	136
Species	"1570291"	Ebola	133
Species	"2697049"	severe acute respiratory syndrome coronavirus 2	126
Species	"9606"	participants	125
Species	"11520"	influenza	124
Species	"191496"	clinical	117
Species	"11118"	Coronavirus	114
Species	"10090"	mouse	110
Species	"11309"	influenza	109
Species	"2697049"	nCoV	107
Species	"2501931"	HCoVs	106
Species	"290028"	HKU1	100
Species	"10090"	mice	99
Species	"31631"	OC43	98
Species	"1335626"	Middle East respiratory syndrome coronavirus	95
Species	"2501931"	human coronaviruses	89
Species	"277944"	NL63	87
Species	"11676"	HIV-1	86
Species	"11137"	"229E"	84

Top Gene Instances

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX fhir: <http://hl7.org/fhir/>
PREFIX pmc: <https://www.ncbi.nlm.nih.gov/pmc/articles#>
select distinct ?pmc_type ?pmc_identifier ?text (count(?text) as ?count) where { 
    ?pmc pmc:annotations ?annotations .
    ?annotations pmc:infons ?pmc_infons .
    ?pmc_infons pmc:identifier ?pmc_identifier .
    ?pmc_infons pmc:type ?pmc_type .
    ?annotations pmc:text ?text .
    FILTER (?pmc_type='Gene').
    
    
} group by ?pmc_type ?pmc_identifier ?text order by DESC(?count)

?pmc_type	?pmc_identifier	?text	?count
Gene	"59272"	ACE2	859
Gene	"6301"	SARS	231
Gene	"3569"	IL-6	145
Gene	"7373"	und	136
Gene	"59272"	hACE2	118
Gene	"1401"	C-reactive protein	86
Gene	"5045"	furin	74
Gene	"1401"	CRP	54
Gene	"3635"	ship	51
Gene	"56925"	muM	50
Gene	"570"	bat	50
Gene	"50528"	TMPRSS2	43
Gene	"7448"	S protein	43
Gene	"11019"	las	41
Gene	"920"	CD4	41
Gene	"7448"	S-protein	40
Gene	"100408882"	ACE2	38
Gene	"59272"	angiotensin-converting enzyme 2	37
Gene	"26503"	AST	34
Gene	"70008"	ACE2	34
Gene	"5447"	por	33
Gene	"925"	CD8	33
Gene	"51257"	March 2	31
Gene	"114548"	NLRP3	28
Gene	"102191832"	Dear	27
Gene	"260431"	COPD	27
Gene	"51316"	C15	27
Gene	"59272"	Angiotensin-converting enzyme 2	27
Gene	"7113"	TMPRSS2	25
Gene	"14254594"	S protein	23
Gene	"162333"	March 10	22
Gene	"28938"	L-1	22
Gene	"1508"	apps	21
Gene	"220972"	March 8	21
Gene	"2875"	alanine aminotransferase	21
Gene	"441061"	March 11	20
Gene	"3570"	IL-6R	18
Gene	"55016"	March 1	18
Gene	"1803"	CD26	17
Gene	"3552"	IL-1beta	17
Gene	"1636"	ACE	16
Gene	"1803"	DPP4	16
Gene	"59272"	ACE-2	16
Gene	"966"	min-1	16
Gene	"551"	vasopressin	15
Gene	"92979"	March 9	15
Gene	"7124"	TNFalpha	14
Gene	"100271923"	Feb 10	13
Gene	"1803"	hDPP4	13
Gene	"22848"	AAK1	13

Top Chemical Instances

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX fhir: <http://hl7.org/fhir/>
PREFIX pmc: <https://www.ncbi.nlm.nih.gov/pmc/articles#>
select distinct ?pmc_type ?pmc_identifier ?text (count(?text) as ?count) where { 
    ?pmc pmc:annotations ?annotations .
    ?annotations pmc:infons ?pmc_infons .
    ?pmc_infons pmc:identifier ?pmc_identifier .
    ?pmc_infons pmc:type ?pmc_type .
    ?annotations pmc:text ?text .
    FILTER (?pmc_type='Chemical').
    
    
} group by ?pmc_type ?pmc_identifier ?text order by DESC(?count)

?pmc_type	?pmc_identifier	?text	?count
Chemical	MESH:D010100	oxygen	210
Chemical	MESH:D019438	ritonavir	193
Chemical	MESH:D061466	lopinavir	175
Chemical	MESH:D002738	chloroquine	163
Chemical	MESH:D008550	melatonin	113
Chemical	MESH:C112485	GA	101
Chemical	MESH:D006886	hydroxychloroquine	91
Chemical	MESH:D002738	Chloroquine	57
Chemical	MESH:D012254	ribavirin	57
Chemical	MESH:D053139	oseltamivir	53
Chemical	MESH:D061466	Lopinavir	52
Chemical	MESH:D002738	CQ	51
Chemical	MESH:D006886	HCQ	50
Chemical	MESH:D014867	water	48
Chemical	MESH:D009534	niclosamide	46
Chemical	MESH:D008550	Melatonin	45
Chemical	C000606551	remdesivir	38
Chemical	MESH:D012254	Ribavirin	38
Chemical	MESH:D000069474	Sofosbuvir	34
Chemical	MESH:D013994	tilorone	33
Chemical	C000606551	Remdesivir	32
Chemical	-	DMEM	30
Chemical	MESH:D013994	Tilorone	29
Chemical	-	FiO2	28
Chemical	MESH:D009534	Niclosamide	28
Chemical	-	PaO2	25
Chemical	-	NIPPV	24
Chemical	MESH:C502936	tocilizumab	23
Chemical	MESH:D005947	glucose	23
Chemical	MESH:D006160	GTP	22
Chemical	MESH:D019438	Ritonavir	22
Chemical	-	Wuhan	20
Chemical	MESH:C023676	chloroquine phosphate	20
Chemical	MESH:D006886	Hydroxychloroquine	20
Chemical	-	SARS-S	19
Chemical	MESH:D000438	alcohol	19
Chemical	MESH:C502936	TCZ	18
Chemical	MESH:D004121	DMSO	18
Chemical	MESH:D006859	hydrogen	18
Chemical	MESH:D013256	steroid	18
Chemical	MESH:D002104	Cd	17
Chemical	MESH:D009638	norepinephrine	17
Chemical	MESH:D013256	steroids	17
Chemical	-	CO2	16
Chemical	MESH:C041747	nitazoxanide	16
Chemical	MESH:C086979	arbidol	16
Chemical	MESH:C502936	Tocilizumab	15
Chemical	MESH:D003404	creatinine	15
Chemical	MESH:D013307	streptomycin	15
Chemical	-	CS	14
Chemical	-	remdesivir	14
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