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tascu.tsv.ttl
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4026 lines (3639 loc) · 161 KB
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@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
<https://tascu.vtt.fi/data/1>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
1 ;
<http://tascu.vtt.fi/ontology/name>
"Select host and product" .
<https://tascu.vtt.fi/data/2>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"J-L: QSAR (prediction of properties from structure)." ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
2 ;
<http://tascu.vtt.fi/ontology/name>
"Obtain relevant data for product" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/1> .
<https://tascu.vtt.fi/data/3>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
3 ;
<http://tascu.vtt.fi/ontology/name>
"Obtain physicochemical data (Toxicity, Solubility, InChI,…) for product" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/2> .
<https://tascu.vtt.fi/data/4>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"@Jean-Loup has a tool for toxicity estimation, training data available only for E. coli. For WP7, it is also important to know where the toxicity database is, what kind of access rights etc." ;
<http://tascu.vtt.fi/ontology/id>
4 ;
<http://tascu.vtt.fi/ontology/name>
"Estimate product toxicity for chassis" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/2> .
<https://tascu.vtt.fi/data/5>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Comments: In principle, most of the design pipeline needs to have been executed for the selection of a good host for a selected product." ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
5 ;
<http://tascu.vtt.fi/ontology/name>
"Obtain relevant data for host" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/1> .
<https://tascu.vtt.fi/data/6>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
6 ;
<http://tascu.vtt.fi/ontology/name>
"Genetic tools" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/5> .
<https://tascu.vtt.fi/data/7>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
7 ;
<http://tascu.vtt.fi/ontology/name>
"Genome sequence" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/5> .
<https://tascu.vtt.fi/data/8>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Strain specific GEMs may be needed for some organisms" ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
8 ;
<http://tascu.vtt.fi/ontology/name>
"Genome-scale metabolic model (GEM)" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/5> .
<https://tascu.vtt.fi/data/9>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
9 ;
<http://tascu.vtt.fi/ontology/name>
"Collect relevant available (bibliographic, experimental) data (candidate ‘sink’ metabolites)" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/5> .
<https://tascu.vtt.fi/data/10>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
10 ;
<http://tascu.vtt.fi/ontology/name>
"Physiological constraints" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/5> .
<https://tascu.vtt.fi/data/11>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
11 ;
<http://tascu.vtt.fi/ontology/name>
"Oxygen requirements" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/10> .
<https://tascu.vtt.fi/data/12>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
12 ;
<http://tascu.vtt.fi/ontology/name>
"Raw material requirements" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/10> .
<https://tascu.vtt.fi/data/13>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"@Jean-Loup has a tool for toxicity estimation, training data available only for E. coli" ;
<http://tascu.vtt.fi/ontology/id>
13 ;
<http://tascu.vtt.fi/ontology/name>
"Estimate product toxicity for chassis" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/10> .
<https://tascu.vtt.fi/data/14>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
14 ;
<http://tascu.vtt.fi/ontology/name>
"Process constraints" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/5> .
<https://tascu.vtt.fi/data/15>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
15 ;
<http://tascu.vtt.fi/ontology/name>
"Technoeconomic constraints" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/1> .
<https://tascu.vtt.fi/data/16>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
16 ;
<http://tascu.vtt.fi/ontology/name>
"Estimate market value of product" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/15> .
<https://tascu.vtt.fi/data/17>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
17 ;
<http://tascu.vtt.fi/ontology/name>
"Intellectual Property (IP) constraints" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/15> .
<https://tascu.vtt.fi/data/18>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
18 ;
<http://tascu.vtt.fi/ontology/name>
"DSP considerations" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/15> .
<https://tascu.vtt.fi/data/19>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
19 ;
<http://tascu.vtt.fi/ontology/name>
"Chassis, substrate, pathway, and product selection" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/1> .
<https://tascu.vtt.fi/data/20>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
20 ;
<http://tascu.vtt.fi/ontology/name>
"Estimate economic feasibility (depends on substrate, pathway, and product)" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/19> .
<https://tascu.vtt.fi/data/21>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
21 ;
<http://tascu.vtt.fi/ontology/name>
"Selection of chassis, substrate, pathway, and product" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/19> .
<https://tascu.vtt.fi/data/22>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
22 ;
<http://tascu.vtt.fi/ontology/name>
"Design" .
<https://tascu.vtt.fi/data/23>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Check that the prerequisites for Computational Strain Design are fulfilled, i.e. the input includes a SBML for the host, the SBML contains a biomass/growth objective, and that the product is specified with sufficient detail (stereochemistry, chain length, etc)." ;
<http://tascu.vtt.fi/ontology/id>
23 ;
<http://tascu.vtt.fi/ontology/name>
"Receive input from \"select host and products\" step" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/22> .
<https://tascu.vtt.fi/data/331>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
331 ;
<http://tascu.vtt.fi/ontology/name>
"Receive name of production host" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/23> .
<https://tascu.vtt.fi/data/332>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
332 ;
<http://tascu.vtt.fi/ontology/name>
"Obtain SBML models for production hosts" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/23> .
<https://tascu.vtt.fi/data/333>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
333 ;
<http://tascu.vtt.fi/ontology/name>
"Obtain annotated genomes of production hosts" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/23> .
<https://tascu.vtt.fi/data/334>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
334 ;
<http://tascu.vtt.fi/ontology/name>
"Receive name of product" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/23> .
<https://tascu.vtt.fi/data/24>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
24 ;
<http://tascu.vtt.fi/ontology/name>
"Receive input from #Upscale #Test-HighThroughput #Test-Bioreactor and #build" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/22> .
<https://tascu.vtt.fi/data/25>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
25 ;
<http://tascu.vtt.fi/ontology/name>
"Physiological constraints" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/24> .
<https://tascu.vtt.fi/data/26>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
26 ;
<http://tascu.vtt.fi/ontology/name>
"Oxygen requirements, pH, solvent, carbon source, substrate and product toxicity, product related energetics, light, temperature" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/25> .
<https://tascu.vtt.fi/data/27>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"(TODO write the steps @NTUA)" ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
27 ;
<http://tascu.vtt.fi/ontology/name>
"Process constraints." ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/24> .
<https://tascu.vtt.fi/data/28>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Product separation requirements; e.g. low pH, minimum titer, unwanted side products that significantly increase the separation cost, etc." ;
<http://tascu.vtt.fi/ontology/id>
28 ;
<http://tascu.vtt.fi/ontology/name>
"Pressure, ..." ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/27> .
<https://tascu.vtt.fi/data/29>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
29 ;
<http://tascu.vtt.fi/ontology/name>
"Execution of Design" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/22> .
<https://tascu.vtt.fi/data/30>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"We might need to rethink this 'Design the chassis' step. Right now it is a bit chaotic and some of the steps inside it are copies of steps mentioned elsewhere. This step can be divided in two parts: 1) deletion of genes; 2) addition of genes. Both parts will contain mandatory genes and genes that could be beneficial (we need some sort of filter or quality check to distinguish between them) . These two types of genes need different follow-up steps. Who is responsible for this step? Maybe they could take a look at it?" ;
<http://tascu.vtt.fi/ontology/id>
30 ;
<http://tascu.vtt.fi/ontology/name>
"Design production strain" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/29> .
<https://tascu.vtt.fi/data/300>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Read literature on known production pathways. -Which reactions are problematic? -What hurdles have they encountered (and how was it solved)? -Compound toxicity? -Enzyme promisquity? Databases -KEGG: pathways, reactions, cofactors, promisquity, known ko/genes, in which organisms are enzymes for those reactions known? -MetaCyc: pathways, reactions, cofactors, promisquity, known/predicted organisms, deltaG? -BRENDA: known substrates, organisms, activators, inhibitors, binding constants, pH optimum, pH tolerance, rate information, mutations" ;
<http://tascu.vtt.fi/ontology/description>
"Read literature on known production pathways and search for data in databases." ;
<http://tascu.vtt.fi/ontology/id>
300 ;
<http://tascu.vtt.fi/ontology/name>
"Information search" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/30> .
<https://tascu.vtt.fi/data/326>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
326 ;
<http://tascu.vtt.fi/ontology/name>
"Freedom to operate (IPR considerations)" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/300> .
<https://tascu.vtt.fi/data/327>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
327 ;
<http://tascu.vtt.fi/ontology/name>
"Known pathways in literature" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/300> .
<https://tascu.vtt.fi/data/330>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
330 ;
<http://tascu.vtt.fi/ontology/name>
"Known pathways in reaction databases" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/300> .
<https://tascu.vtt.fi/data/328>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"Search patent literature for similar pathways and individual modifications." ;
<http://tascu.vtt.fi/ontology/id>
328 ;
<http://tascu.vtt.fi/ontology/name>
"Patent search" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/300> .
<https://tascu.vtt.fi/data/31>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
31 ;
<http://tascu.vtt.fi/ontology/name>
"Computational metabolic design" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/30> .
<https://tascu.vtt.fi/data/32>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
32 ;
<http://tascu.vtt.fi/ontology/name>
"Computational product pathway design" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/31> .
<https://tascu.vtt.fi/data/33>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Convert RetroPath output to complete reactions. Check MetaNetX reactions for correctness and electron balancing. For every unknown cofactor, propose plausible cofactors for the chassis considered." ;
<http://tascu.vtt.fi/ontology/id>
33 ;
<http://tascu.vtt.fi/ontology/name>
"Enumerate pathway options (Retropath,…)" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/32> .
<https://tascu.vtt.fi/data/34>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
34 ;
<http://tascu.vtt.fi/ontology/name>
"Screen pathway options based on quality criteria" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/33> .
<https://tascu.vtt.fi/data/321>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
321 ;
<http://tascu.vtt.fi/ontology/name>
"Convert reaction rules to complete reactions" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/32> .
<https://tascu.vtt.fi/data/322>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"E.g. define cofactors where cofactors are unknown." ;
<http://tascu.vtt.fi/ontology/id>
322 ;
<http://tascu.vtt.fi/ontology/name>
"Refine pathways" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/32> .
<https://tascu.vtt.fi/data/35>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Score pathways. Estimate e.g. membrane toxicity of pathway intermediates. Estimate thermodynamic feasibility of reactions in pathway. If necessary, use OBE to find distributed bottlenecks." ;
<http://tascu.vtt.fi/ontology/id>
35 ;
<http://tascu.vtt.fi/ontology/name>
"Score pathways without chassis" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/32> .
<https://tascu.vtt.fi/data/39>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
39 ;
<http://tascu.vtt.fi/ontology/name>
"Membrane toxicity of intermediates" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/35> .
<https://tascu.vtt.fi/data/38>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Use eQuilibrator if no other tool available for pH-dependent thermodynamics." ;
<http://tascu.vtt.fi/ontology/id>
38 ;
<http://tascu.vtt.fi/ontology/name>
"Thermodynamic feasibility verification" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/35> .
<https://tascu.vtt.fi/data/323>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Optional" ;
<http://tascu.vtt.fi/ontology/id>
323 ;
<http://tascu.vtt.fi/ontology/name>
"Optimized Bottleneck Energetics" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/35> .
<https://tascu.vtt.fi/data/40>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
40 ;
<http://tascu.vtt.fi/ontology/name>
"Chassis embedment" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/31> .
<https://tascu.vtt.fi/data/41>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
41 ;
<http://tascu.vtt.fi/ontology/name>
"Receive input from product pathway design" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/40> .
<https://tascu.vtt.fi/data/42>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
42 ;
<http://tascu.vtt.fi/ontology/name>
"Map metabolites between pathway and chassis" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/40> .
<https://tascu.vtt.fi/data/36>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Add pathway to SBML for chassis. Match pathway metabolites to chassis metabolites. Verify matches by structural comparison. Also check stereochemistry. Prefer starting pathways from cytosolic metabolites. If pathway generates side products, i.e. compounds that aren't chassis metabolites, find the reactions that connects them to the metabolic network of the chassis." ;
<http://tascu.vtt.fi/ontology/id>
36 ;
<http://tascu.vtt.fi/ontology/name>
"Add production pathway to chassis SBML in silico" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/40> .
<https://tascu.vtt.fi/data/316>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
316 ;
<http://tascu.vtt.fi/ontology/name>
"Fill metabolic gaps" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/40> .
<https://tascu.vtt.fi/data/37>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
37 ;
<http://tascu.vtt.fi/ontology/name>
"Screen potential substrates in silico" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/40> .
<https://tascu.vtt.fi/data/44>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Anaerobic, aerobic, peroxisome active/inactive, etc." ;
<http://tascu.vtt.fi/ontology/id>
44 ;
<http://tascu.vtt.fi/ontology/name>
"Screen growth conditions" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/40> .
<https://tascu.vtt.fi/data/45>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
45 ;
<http://tascu.vtt.fi/ontology/name>
"Growth-product coupling. (e.g. OptKnock, RobustKnock, Minimal Cut Sets)" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/40> .
<https://tascu.vtt.fi/data/49>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Check that oxygen consumption is reasonable. VTT has a SOP" ;
<http://tascu.vtt.fi/ontology/id>
49 ;
<http://tascu.vtt.fi/ontology/name>
"Calculate expected yields" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/40> .
<https://tascu.vtt.fi/data/317>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
317 ;
<http://tascu.vtt.fi/ontology/name>
"Estimate productivities" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/40> .
<https://tascu.vtt.fi/data/324>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
324 ;
<http://tascu.vtt.fi/ontology/name>
"Evaluate and choose pathways" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/31> .
<https://tascu.vtt.fi/data/52>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"The remaining tasks relating to enzyme design could be moved to enzyme design." ;
<http://tascu.vtt.fi/ontology/id>
52 ;
<http://tascu.vtt.fi/ontology/name>
"Genetic design for chassis" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/30> .
<https://tascu.vtt.fi/data/43>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"(e.g. genome re-annotation, literature search. Find the enzymes of the metabolites from the reference databases, and look in the genome whether homologous enzymes exist natively)." ;
<http://tascu.vtt.fi/ontology/id>
43 ;
<http://tascu.vtt.fi/ontology/name>
"Check for native enzymes with activity for heterologous metabolites" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/52> .
<https://tascu.vtt.fi/data/72>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
72 ;
<http://tascu.vtt.fi/ontology/name>
"Genome reannotation" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/43> .
<https://tascu.vtt.fi/data/46>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
46 ;
<http://tascu.vtt.fi/ontology/name>
"Search for native homologues of enzymes acting on the heterologous metabolites" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/43> .
<https://tascu.vtt.fi/data/50>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
50 ;
<http://tascu.vtt.fi/ontology/name>
"Additional trait design" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/52> .
<https://tascu.vtt.fi/data/47>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
47 ;
<http://tascu.vtt.fi/ontology/name>
"Propose desirable traits" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/50> .
<https://tascu.vtt.fi/data/51>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
51 ;
<http://tascu.vtt.fi/ontology/name>
"Bioprospecting for traits" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/50> .
<https://tascu.vtt.fi/data/48>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
48 ;
<http://tascu.vtt.fi/ontology/name>
"Pathway improvement by mutations, supporting/auxiliary pathways, enzymes/cofactor specificity, genetic modifications" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/52> .
<https://tascu.vtt.fi/data/71>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
71 ;
<http://tascu.vtt.fi/ontology/name>
"Select promoter types" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/52> .
<https://tascu.vtt.fi/data/54>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
54 ;
<http://tascu.vtt.fi/ontology/name>
"Evaluate and choose strains" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/52> .
<https://tascu.vtt.fi/data/325>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
325 ;
<http://tascu.vtt.fi/ontology/name>
"Describe genetic constructs in SBOL format" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/52> .
<https://tascu.vtt.fi/data/74>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
74 ;
<http://tascu.vtt.fi/ontology/name>
"Store the list of enzyme functions" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/30> .
<https://tascu.vtt.fi/data/318>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
318 ;
<http://tascu.vtt.fi/ontology/name>
"Store the list of gene deletions" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/30> .
<https://tascu.vtt.fi/data/319>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
319 ;
<http://tascu.vtt.fi/ontology/name>
"Store the list of genotypes" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/30> .
<https://tascu.vtt.fi/data/320>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
320 ;
<http://tascu.vtt.fi/ontology/name>
"Store the list of promoter types" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/30> .
<https://tascu.vtt.fi/data/73>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"This should serve also enzyme screening and protein production; should be expanded if these other applications are relevant. #EnzymeDesign." ;
<http://tascu.vtt.fi/ontology/id>
73 ;
<http://tascu.vtt.fi/ontology/name>
"Select and/or design enzyme" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/29> .
<https://tascu.vtt.fi/data/75>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
75 ;
<http://tascu.vtt.fi/ontology/name>
"TODO write the steps @INRA" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/73> .
<https://tascu.vtt.fi/data/307>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
307 ;
<http://tascu.vtt.fi/ontology/name>
"Retrieve the list of enzyme functions" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/73> .
<https://tascu.vtt.fi/data/56>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"#RoundRobinNeeded but comparison difficult" ;
<http://tascu.vtt.fi/ontology/id>
56 ;
<http://tascu.vtt.fi/ontology/name>
"Generate candidate sequences (Enzyme search)" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/73> .
<https://tascu.vtt.fi/data/58>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
58 ;
<http://tascu.vtt.fi/ontology/name>
"Function-based in silico screening of candidate sequences" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/73> .
<https://tascu.vtt.fi/data/55>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
55 ;
<http://tascu.vtt.fi/ontology/name>
"Choose enzyme sequences" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/73> .
<https://tascu.vtt.fi/data/57>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
57 ;
<http://tascu.vtt.fi/ontology/name>
"Optimize gene sequences" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/73> .
<https://tascu.vtt.fi/data/59>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
59 ;
<http://tascu.vtt.fi/ontology/name>
"Remove mobile regulatory elements" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/73> .
<https://tascu.vtt.fi/data/60>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
60 ;
<http://tascu.vtt.fi/ontology/name>
"Send list of gene additions" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/73> .
<https://tascu.vtt.fi/data/301>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"Applies equally to production strains, enzyme screening hosts, and protein production hosts." ;
<http://tascu.vtt.fi/ontology/id>
301 ;
<http://tascu.vtt.fi/ontology/name>
"Design DNA constructs for expression host" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/29> .
<https://tascu.vtt.fi/data/53>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
53 ;
<http://tascu.vtt.fi/ontology/name>
"Freedom to operate with regards to the tools #IPRConsiderations" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/301> .
<https://tascu.vtt.fi/data/308>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
308 ;
<http://tascu.vtt.fi/ontology/name>
"Retrieve the list of gene deletions" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/301> .
<https://tascu.vtt.fi/data/309>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
309 ;
<http://tascu.vtt.fi/ontology/name>
"Retrieve the list of gene additions" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/301> .
<https://tascu.vtt.fi/data/310>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"All cargo defined earlier based on modeling desired phenotype." ;
<http://tascu.vtt.fi/ontology/id>
310 ;
<http://tascu.vtt.fi/ontology/name>
"Retrieve the list of promoter types" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/301> .
<https://tascu.vtt.fi/data/311>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"May be combinatorial." ;
<http://tascu.vtt.fi/ontology/id>
311 ;
<http://tascu.vtt.fi/ontology/name>
"Select promoters" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/301> .
<https://tascu.vtt.fi/data/312>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/comment>
"May be combinatorial." ;
<http://tascu.vtt.fi/ontology/id>
312 ;
<http://tascu.vtt.fi/ontology/name>
"Select integration sites/loci" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/301> .
<https://tascu.vtt.fi/data/61>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
61 ;
<http://tascu.vtt.fi/ontology/name>
"Select genome editing strategy" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/301> .
<https://tascu.vtt.fi/data/62>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
62 ;
<http://tascu.vtt.fi/ontology/name>
"CRISPR/Cas9 #SopNeeded" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/61> .
<https://tascu.vtt.fi/data/63>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
63 ;
<http://tascu.vtt.fi/ontology/name>
"MAGE: genome engineering #SopNeeded" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/61> .
<https://tascu.vtt.fi/data/313>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
313 ;
<http://tascu.vtt.fi/ontology/name>
"Select vectors/plasmids/DNA constructs" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/301> .
<https://tascu.vtt.fi/data/64>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/id>
64 ;
<http://tascu.vtt.fi/ontology/name>
"Select vector assembly strategy" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/301> .
<https://tascu.vtt.fi/data/65>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
65 ;
<http://tascu.vtt.fi/ontology/name>
"SEVA/METABRICK, Moclo, Gibson pathway engineering @Wageningen" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/64> .
<https://tascu.vtt.fi/data/66>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;
<http://tascu.vtt.fi/ontology/id>
66 ;
<http://tascu.vtt.fi/ontology/name>
"#TODO add the list of tasks needed #ToBeReviewed" ;
<http://tascu.vtt.fi/ontology/parent>
<https://tascu.vtt.fi/data/65> .
<https://tascu.vtt.fi/data/67>
a <http://tascu.vtt.fi/ontology/Step> ;
<http://tascu.vtt.fi/ontology/description>
"NULL" ;