Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add bath terms #1845

Merged
merged 2 commits into from
Jan 6, 2025
Merged

Add bath terms #1845

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
6746444
Add bath terms
sebastianduesing Dec 9, 2024
63a71d9
Merge branch 'master' into 1585_new_bath_terms
jamesaoverton Jan 6, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
68 changes: 68 additions & 0 deletions src/ontology/modules/devices.owl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9299,6 +9299,74 @@



<!-- http://purl.obolibrary.org/obo/OBI_0003688 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003688">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400120"/>
<obo:IAO_0000111>sand bath</obo:IAO_0000111>
<obo:IAO_0000112>A sand bath was used to provide even heating of the round-bottom flask at elevated temperatures.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A temperature control bath in which sand acts as contact medium for the temperature transfer (from heating or cooling elements to the sample).</obo:IAO_0000115>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000117>https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)</obo:IAO_0000117>
<obo:IAO_0000119>Based on OBI:0400157</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1585</obo:IAO_0000233>
<obo:IAO_0000234>https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)</obo:IAO_0000234>
<rdfs:label>sand bath</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003689 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003689">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400120"/>
<obo:IAO_0000111>ice bath</obo:IAO_0000111>
<obo:IAO_0000112>A brine water ice bath was used to keep the reaction below 0 degrees Celsius.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A temperature control bath in which a water ice mixture acts as contact medium at constant temperature of 0 degrees Celsius or below if salt solutions are used.</obo:IAO_0000115>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000117>https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)</obo:IAO_0000117>
<obo:IAO_0000119>Based on OBI:0400157</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1585</obo:IAO_0000233>
<obo:IAO_0000234>https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)</obo:IAO_0000234>
<rdfs:label>ice bath</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003690 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003690">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400120"/>
<obo:IAO_0000111>dry ice bath</obo:IAO_0000111>
<obo:IAO_0000112>A dry ice bath using ethylene glycol was used to maintain a temperature of -10 degrees Celsius.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A temperature control bath in which a dry ice solvent mixture acts as contact medium at a constant temperatures significantly below 0 degrees Celsius.</obo:IAO_0000115>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000117>https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)</obo:IAO_0000117>
<obo:IAO_0000119>Based on OBI:0400157</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1585</obo:IAO_0000233>
<obo:IAO_0000234>https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)</obo:IAO_0000234>
<rdfs:label>dry ice bath</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003691 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003691">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400120"/>
<obo:IAO_0000111>liquid nitrogen bath</obo:IAO_0000111>
<obo:IAO_0000112>A liquid nitrogen bath is used to adsorb helium gas on samples for surface area measurements.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A temperature control bath in which liquid nitrogen acts as contact medium providing a constant temperature of −195.8 °C at 1 atm.</obo:IAO_0000115>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000117>https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)</obo:IAO_0000117>
<obo:IAO_0000119>Based on OBI:0400157</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1585</obo:IAO_0000233>
<obo:IAO_0000234>https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)</obo:IAO_0000234>
<rdfs:label>liquid nitrogen bath</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0302886 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0302886"/>
Expand Down
6 changes: 4 additions & 2 deletions src/ontology/templates/devices.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -318,9 +318,7 @@ OBI:0001974 Ion 314 Chip v2 Ion 314 Chip v2 Ion PGM 314 Chip|Ion 314 Chip|Ion P
OBI:0002000 Illumina Genome Analyzer IIx metadata complete Illumina GA IIx|Genome Analyzer IIx An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. ENCODE group Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. ""Lane-by-lane sequencing using Illumina's Genome Analyzer II."" BioTechniques 54.5 (2013): 265-269. PMID: 23662897 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina Genome Analyzer II Illumina
OBI:0002001 Illumina HiSeq 2000 metadata complete HiSeq 2000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina HiSeq series instrument Illumina
OBI:0002002 Illumina HiSeq 2500 metadata complete HiSeq 2500 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf Spaethling, Jennifer M., and James H. Eberwine. ""Single-cell transcriptomics for drug target discovery."" Current opinion in pharmacology (2013). pmid:23725882 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina HiSeq series instrument Illumina

OBI:0002003 Illumina MiSeq metadata complete MiSeq A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301] PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng DNA sequencer Illumina

OBI:0002004 Methylation 450K BeadChip metadata complete Illumina Infinium Human Methylation 450K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn Naumov, Vladimir A., et al. ""Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips."" Epigenetics 8.9 (2013): 0-1. PMID: 23867710 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip
OBI:0002005 Methylation 27K BeadChip metadata complete Illumina Infinium Human Methylation 27K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf Polidoro, Silvia, et al. ""Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw."" Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip
OBI:0002006 1M-Duo Infinium HD BeadChip metadata complete Illumina Human 1M-Duo Infinium HD BeadChip A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. http://www.illumina.com/technology/infinium_hd_assay.ilmn Edwards, Todd L., et al. ""Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease."" Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina BeadChip
Expand Down Expand Up @@ -476,6 +474,10 @@ OBI:0003664 Illumina NovaSeq X Plus Illumina NovaSeq X Plus NovaSeq X System|No
OBI:0003683 Illumina HiSeq series instrument metadata incomplete HiSeq series A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word HiSeq. PERSON: Mark Andrew Miller https://www.illumina.com/content/dam/illumina-support/documents//products/datasheets/datasheet_hiseq_systems.pdf PERSON: Mark Andrew Miller This class represents a series of instruments with various model names. There are several models in this series, including one that was simply called “HiSeq” as the model name. GENEPIO:0100110 ‘Illumina HiSeq’ may refer to a model, not the series. OBI may not have classes for all of the instruments in this series. Alicia Clum https://github.com/obi-ontology/obi/issues/1825 DNA sequencer Illumina
OBI:0003684 Illumina NextSeq series instrument metadata incomplete NextSeq series A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NextSeq. PERSON: Mark Andrew Miller https://www.cd-genomics.com/blog/nextseq/ PERSON: Mark Andrew Miller This class represents a series of instruments with various model names. There are several models in this series. OBI may not have classes for all of the instruments in this series. It is unclear whether GENEPIO:0100126 ’Illumina NextSeq’ refers to the series or a model. Alicia Clum https://github.com/obi-ontology/obi/issues/1825 DNA sequencer Illumina
OBI:0003685 Illumina NovaSeq series instrument metadata incomplete NovaSeq series A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NovaSeq. PERSON: Mark Andrew Miller PERSON: Mark Andrew Miller This class represents a series of instruments with various model names. There are several models in this series. OBI may not have classes for all of the instruments in this series. It is unclear whether GENEPIO:0100122 ‘Illumina NovaSeq’ refers to the series or to a model. Alicia Clum https://github.com/obi-ontology/obi/issues/1825 DNA sequencer Illumina
OBI:0003688 sand bath sand bath A temperature control bath in which sand acts as contact medium for the temperature transfer (from heating or cooling elements to the sample). Based on OBI:0400157 A sand bath was used to provide even heating of the round-bottom flask at elevated temperatures. https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)|Sebastian Duesing https://orcid.org/0000-0002-8786-1756 (Schafer, Wes) https://github.com/obi-ontology/obi/issues/1585 subclass temperature control bath
OBI:0003689 ice bath ice bath A temperature control bath in which a water ice mixture acts as contact medium at constant temperature of 0 degrees Celsius or below if salt solutions are used. Based on OBI:0400157 A brine water ice bath was used to keep the reaction below 0 degrees Celsius. https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)|Sebastian Duesing https://orcid.org/0000-0002-8786-1756 (Schafer, Wes) https://github.com/obi-ontology/obi/issues/1585 subclass temperature control bath
OBI:0003690 dry ice bath dry ice bath A temperature control bath in which a dry ice solvent mixture acts as contact medium at a constant temperatures significantly below 0 degrees Celsius. Based on OBI:0400157 A dry ice bath using ethylene glycol was used to maintain a temperature of -10 degrees Celsius. https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)|Sebastian Duesing https://orcid.org/0000-0002-8786-1756 (Schafer, Wes) https://github.com/obi-ontology/obi/issues/1585 subclass temperature control bath
OBI:0003691 liquid nitrogen bath liquid nitrogen bath A temperature control bath in which liquid nitrogen acts as contact medium providing a constant temperature of −195.8 °C at 1 atm. Based on OBI:0400157 A liquid nitrogen bath is used to adsorb helium gas on samples for surface area measurements. https://orcid.org/0000-0002-8786-1756 (Schafer, Wes)|Sebastian Duesing https://orcid.org/0000-0002-8786-1756 (Schafer, Wes) https://github.com/obi-ontology/obi/issues/1585 subclass temperature control bath
OBI:0400005 A10-Analyzer A10-Analyzer ready for release A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer
OBI:0400006 A40-MiniFCM A40-MiniFCM ready for release A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer
OBI:0400007 analog-to-digital converter analog-to-digital converter metadata incomplete A2D|A-D An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. http://en.wiktionary.org/wiki/Analog-to-Digital_Converter The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. John Quinn|Melanie Courtot device signal conversion function
Expand Down
Loading