marcin p. joachimiak

icon company Lawrence Berkeley National Laboratory icon location Staff Researcher and Software Developer at LBNL. Interests: Computational Biology / Systems Biology / Machine Learning / Deep Learning / Knowledge Graphs

Results 148 issues of marcin p. joachimiak

review bacdive isolation sources, some could be tags

e.g. Inflammation

transfer obsolete EC nodes to replacement

EC ontology transform truncates .- in ECs

EC:2.7.8 should be EC:2.7.8.- EC:2.7.8 biolink:Enzyme Transferases for other substituted phosphate groups ec.json http://purl.obolibrary.org/obo/EC_2.7.8

nodes with spaces in ids

grep -E '^.*:.* .* biolink:' merged-kg_nodes.tsv 75 of these, including: https://github.com/Knowledge-Graph-Hub/kg-microbe/issues/264 and cell_shape:disc biolink:AbstractEntity disc Graph

assay: nodes with spaces in id

74 of these: assay:API_20E_TDA Trp biolink:PhenotypicQuality API 20E - TDA Trp Graph assay:API_20E_LDC Lys biolink:PhenotypicQuality API 20E - LDC Lys Graph assay:API_NH_beta GAL biolink:PhenotypicQuality API NH - beta GAL Graph...

cell_shape: has three categories

biolink:PhenotypicQuality biolink:AbstractEntity biolink:AbstractEntity|biolink:PhenotypicQuality

strains and data from JMC

https://jcm.brc.riken.jp/en/catalogue_e

biolog data

https://figshare.com/search?q=%22biolog%22&itemTypes=3 https://datadryad.org/search?utf8=✓&q=%22biolog%22 https://zenodo.org/search?q=%22biolog%22&l=list&p=1&s=10&sort=bestmatch