Releases: Planteome/samara
v0.2.1
v0.2.0
NEW FEATURES
- add PO: term matching for plant parts (see c12bde8)
- exclude turfgrasses for ASPNet scraper
- add explicit name mappings
IMPROVEMENT
- make download log messages less chatty
- add documentation on APSNet scrape process (see https://github.com/jhpoelen/samara/blob/01057adb1db468712f7e96c2ce5e88cfdb88b672/src/main/resources/org/planteome/samara/apsnet/README.md)
- add more potential datasets to source.md (https://github.com/jhpoelen/samara/blob/9df6fd75e0c29d1b56632017794c1ab91f90c9ee/sources.md)
BUG FIXES
n/a
v0.1.10: using first pass at ncbi taxonomy linkout map to resolve taxon ids in…
NEW FEATURES
n/a
IMPROVEMENT
- use ncbi linkout taxon id map to link GRINTaxa scraped from ars-grin (see issue #13)
BUG FIXES
n/a
Attached files were created by samara v0.1.10 on 22 Nov 2016.
The file grin-16k.tsv.gz was created on 22 Nov 2016 using java -jar samara-assembly-0.1.10.jar scrape grin | gzip > grin-16k.tsv.gz on . The scrape can canceled after 16k lines to create a representative example.
v0.1.9
NEW FEATURES
- add ncbi linkout scraper to retrieve ncbi taxa linked to grin taxonomy (see issue #13)
IMPROVEMENT
n/a
BUG FIXES
n/a
Attached files were created by samara on 22 Nov 2016.
The file grin-ncbi_linkout.tsv.gz was created on 22 Nov 2016 using java -jar samara-assembly-0.1.9.jar scrape ncbi_linkout | gzip > grin-ncbi_linkout.tsv.gz on .
v0.1.8
NEW FEATURES
n/a
IMPROVEMENT
- first pass to resolve pathogen/plant names for apsnet (see issue #24)
BUG FIXES
- minor bug fixes in name resolving
Attached files were created by samara on 7 Sept 2016.
The file apsnet.tsv.gz was created on 7 Sept 2016 using java -jar samara-assembly-0.1.8.jar scrape apsnet | gzip > apsnet.tsv.gz
The file grin-16k.tsv.gz was created on 7 Sept 2016 using java -jar samara-assembly-0.1.8.jar scrape grin | gzip > grin-16k.tsv.gz on . The scrape can canceled after 16k lines to create a representative example.
v0.1.7
NEW FEATURES
n/a
IMPROVEMENT
- include verbatim pathogen/host strings from apsnet in export (see issue #28)
- various improvements in pathogen name extraction and expansion in apsnet
- include basic validation for AccessionDetails page (see issue #27)
BUG FIXES
n/a
Attached files were created by samara on 10-11 Aug 2016.
The file apsnet.tsv.gz was created using on 10 Aug 2016 java -jar samara-assembly-0.1.7.jar scrape apsnet | gzip > apsnet.tsv.gz
The file grin.tsv.gz was created over a 2 day period starting on 11 Aug 2015 using command similar to java -jar samara-assembly-0.1.7.jar scrape grin | gzip > grin.tsv.gz on . The scrape took a long about 2.5 days.
v0.1.6
NEW FEATURES
n/a
IMPROVEMENT
- expand pathogen abbreviations in apsnet (see issue #21)
- parse host descriptions in apsnet (see issue #22)
- add source citation apsnet (see issue #23)
BUG FIXES
n/a
Attached files were created by samara on 3 Aug 2016.
The file apsnet.tsv.gz was created using java -jar samara-assembly-0.1.6.jar scrape apsnet | gzip > apsnet.tsv.gz
The file grin-16k.tsv.gz was created using java -jar samara-assembly-0.1.6.jar scrape grin | gzip > grin-16k.tsv.gz. The scrape took a long time and only first 16k observations are included.
v0.1.5: simplified accessionId extraction; mine descriptor name from accessio…
NEW FEATURES
n/a
IMPROVEMENT
- replace whitespaces in grin column names with underscores to facilitate
awkscripting
BUG FIXES
- align descriptor short name with descriptor id/definition (see issue #20)
Attached files were created by samara on 28 July 2016.
The file apsnet.tsv.gz was created using java -jar samara-assembly-0.1.5.jar scrape apsnet | gzip > apsnet.tsv.gz
The file grin-16k.tsv.gz was created using java -jar samara-assembly-0.1.5.jar scrape grin | gzip > grin-16k.tsv.gz. The scrape took a long time and was canceled by exiting the program, resulting in about 16k observations.
v0.1.4
NEW FEATURES
n/a
IMPROVEMENT
- include grin id prefixes in ars-grin accession observation data issue #18
BUG FIXES
n/a
Attached files were created by samara on 27 July 2016.
The file apsnet.tsv.gz was created using java -jar samara-assembly-0.1.4.jar scrape apsnet | gzip > apsnet.tsv.gz
The file grin-16k.tsv.gz was created using java -jar samara-assembly-0.1.4.jar scrape grin | gzip > grin-16k.tsv.gz. The scrape took a long time and was canceled by exiting the program, resulting in about 16k observations.
v0.1.3
NEW FEATURES
n/a
IMPROVEMENT
- include accessor bibliographic references in ars-grin accession observation data issue #15
- include accessor origin in ars-grin accession observation data issue #12
BUG FIXES
n/a
Attached files were created by samara on 27 July 2016.
The file apsnet.tsv.gz was created using java -jar samara-assembly-0.1.3.jar scrape apsnet | gzip > apsnet.tsv.gz
The file grin-16k.tsv.gz was created using java -jar samara-assembly-0.1.3.jar scrape grin | gzip > grin-16k.tsv.gz. The scrape took a long time and was canceled by exiting the program, resulting in about 16k observations.