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TREC COVID Round 3 topics and output of UDel qgen (#1225)
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@lukuang
lukuang authored May 26, 2020
1 parent d6cf46d commit bed8ead
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12 changes: 9 additions & 3 deletions src/main/python/trec-covid/generate_query_udel.py
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Expand Up @@ -27,9 +27,8 @@

# general settings
parser.add_argument('--anserini_root', default='', help='Anserini path')
parser.add_argument('--output_file', help='output path for the query')
parser.add_argument(
'--round', default='1', choices=['1', '2'],
'--round', default='1', choices=['1', '2', '3'],
help='which round the query file should be generated for'
)
args = parser.parse_args()
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original_query_file_name
)

output_query_file_name = f'topics.covid-round{args.round}-udel.xml'
output_query_file = os.path.join(
args.anserini_root,
'src/main/resources/topics-and-qrels',
output_query_file_name
)

root = etree.parse(original_query_file).getroot()
for topic in root:
qid = topic.attrib['number']
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for tag in tags_to_be_removed:
topic.remove(tag)

with open(args.output_file,'wb') as f:
with open(output_query_file,'wb') as f:
f.write(etree.tostring(root))

122 changes: 122 additions & 0 deletions src/main/resources/topics-and-qrels/topics.covid-round3-udel.xml
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<topics task="COVIDSearch 2020" batch="3">
<topic number="1">
<query>coronavirus origin origin COVID-19</query>
</topic>
<topic number="2">
<query>coronavirus response weather changes coronavirus changes weather</query>
</topic>
<topic number="3">
<query>coronavirus immunity SARS-CoV2 infected people immunity cross protection</query>
</topic>
<topic number="4">
<query>people die coronavirus causes death Covid-19</query>
</topic>
<topic number="5">
<query>animal models COVID-19 drugs SARS-CoV SARS-CoV-2 animal studies</query>
</topic>
<topic number="6">
<query>coronavirus test rapid testing rapid testing Covid-19</query>
</topic>
<topic number="7">
<query>serological tests coronavirus serological tests detect antibodies coronavirus</query>
</topic>
<topic number="8">
<query>coronavirus reporting lack testing availability underreporting true incidence Covid-19</query>
</topic>
<topic number="9">
<query>coronavirus Canada COVID-19 affected Canada</query>
</topic>
<topic number="10">
<query>coronavirus social distancing impact social distancing impact slowing spread COVID-19</query>
</topic>
<topic number="11">
<query>coronavirus hospital rationing guidelines triaging patients infected coronavirus</query>
</topic>
<topic number="12">
<query>coronavirus quarantine practices hospitals home quarantine</query>
</topic>
<topic number="13">
<query>coronavirus spread transmission routes coronavirus</query>
</topic>
<topic number="14">
<query>coronavirus super spreaders evidence COVID-19 super spreaders</query>
</topic>
<topic number="15">
<query>coronavirus body long coronavirus live body</query>
</topic>
<topic number="16">
<query>long coronavirus survive surfaces long coronavirus surfaces</query>
</topic>
<topic number="17">
<query>coronavirus clinical trials clinical trials coronavirus</query>
</topic>
<topic number="18">
<query>masks prevent coronavirus masks preventing infection Covid-19</query>
</topic>
<topic number="19">
<query>alcohol sanitizer kills coronavirus type hand sanitizer Covid-19</query>
</topic>
<topic number="20">
<query>coronavirus ACE inhibitors patients Angiotensin-converting enzyme inhibitors ACE increased risk COVID-19</query>
</topic>
<topic number="21">
<query>coronavirus mortality mortality rates populations</query>
</topic>
<topic number="22">
<query>coronavirus heart impacts cardiac complications patients COVID-19</query>
</topic>
<topic number="23">
<query>coronavirus hypertension complications COVID-19 associated with hypertension</query>
</topic>
<topic number="24">
<query>coronavirus diabetes complications COVID-19 associated with diabetes</query>
</topic>
<topic number="25">
<query>coronavirus biomarkers biomarkers severe clinical course 2019-nCOV infection</query>
</topic>
<topic number="26">
<query>coronavirus early symptoms initial symptoms Covid-19</query>
</topic>
<topic number="27">
<query>coronavirus asymptomatic infected Covid-19 asymptomatic</query>
</topic>
<topic number="28">
<query>coronavirus hydroxychloroquine evidence hydroxychloroquine treating Covid-19</query>
</topic>
<topic number="29">
<query>coronavirus drug repurposing SARS-CoV-2 proteins-human proteins interactions potential drug targets drugs information</query>
</topic>
<topic number="30">
<query>coronavirus remdesivir remdesivir effective treatment COVID-19</query>
</topic>
<topic number="31">
<query>difference coronavirus flu coronavirus seasonal flu</query>
</topic>
<topic number="32">
<query>coronavirus subtypes SARS-CoV-2 subtypes</query>
</topic>
<topic number="33">
<query>coronavirus vaccine candidates vaccine candidates tested Covid-19</query>
</topic>
<topic number="34">
<query>coronavirus recovery longer-term complications recover COVID-19</query>
</topic>
<topic number="35">
<query>coronavirus public datasets public datasets COVID-19</query>
</topic>
<topic number="36">
<query>SARS-CoV-2 spike structure protein structure SARS-CoV-2 spike</query>
</topic>
<topic number="37">
<query>SARS-CoV-2 phylogenetic analysis result phylogenetic analysis SARS-CoV-2 genome sequence</query>
</topic>
<topic number="38">
<query>COVID inflammatory response mechanism inflammatory response pathogenesis COVID-19 cases</query>
</topic>
<topic number="39">
<query>COVID-19 cytokine storm mechanism cytokine storm syndrome COVID-19</query>
</topic>
<topic number="40">
<query>coronavirus mutations observed mutations SARS-CoV-2 genome mutations</query>
</topic>
</topics>
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