diff --git a/obi.owl b/obi.owl
index cca42515..6469e90e 100755
--- a/obi.owl
+++ b/obi.owl
@@ -13,7 +13,7 @@
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
-
+
en
Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
@@ -80,7 +80,7 @@
http://creativecommons.org/licenses/by/4.0/
Ontology for Biomedical Investigations
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
- 2024-10-03
+ 2024-10-25
@@ -63793,15 +63793,21 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
- Genome Analyzer IIx
+
+
+
+
+
+
+ Illumina Genome Analyzer IIx
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
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.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
+ Genome Analyzer IIx
Illumina GA IIx
- Illumina Genome Analyzer IIx
ENCODE group
- Genome Analyzer IIx
+ Illumina Genome Analyzer IIx
@@ -63809,7 +63815,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
-
+
@@ -63831,7 +63837,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
-
+
@@ -63860,14 +63866,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
- MiSeq
+ Illumina MiSeq
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]
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.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng
- Illumina MiSeq
+ MiSeq
http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf
- MiSeq
+ Illumina MiSeq
@@ -64749,20 +64755,20 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
-
+
- NextSeq 500
+ Illumina NextSeq 500
A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
- Illumina NextSeq 500
+ NextSeq 500
http://systems.illumina.com/systems/nextseq-sequencer.html
- NextSeq 500
+ Illumina NextSeq 500
@@ -64770,7 +64776,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
-
+
@@ -64883,14 +64889,20 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
- Genome Analyzer IIe
+
+
+
+
+
+
+ Illumina Genome Analyzer IIe
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 IIe makes industry-leading next-generation sequencing technology accessible to more laboratories.
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
+ Genome Analyzer IIe
Illumina GA IIe
- Illumina Genome Analyzer IIe
http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf
- Genome Analyzer IIe
+ Illumina Genome Analyzer IIe
@@ -65462,7 +65474,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
-
+
@@ -65483,7 +65495,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
-
+
@@ -68083,6 +68095,12 @@ https://www.doi.org/
+
+
+
+
+
+
Illumina Genome Analyzer
A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.
@@ -68097,7 +68115,13 @@ https://www.doi.org/
-
+
+
+
+
+
+
+
Illumina HiSeq X Ten
A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.
@@ -77542,7 +77566,7 @@ https://www.doi.org/
-
+
@@ -95132,7 +95156,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
-
+
@@ -95157,7 +95181,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
-
+
@@ -95173,7 +95197,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
https://www.illumina.com/systems/sequencing-platforms/nextseq.html
https://github.com/obi-ontology/obi/issues/1546
gEAR
- NextSeq 550
+ Illumina NextSeq 550
@@ -101858,7 +101882,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
-
+
@@ -103468,7 +103492,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
-
+
@@ -103492,7 +103516,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
-
+
@@ -103589,6 +103613,80 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
+
+
+
+
+
+
+
+
+
+
+ Illumina HiSeq Series Instrument
+ https://www.illumina.com/content/dam/illumina-support/documents//products/datasheets/datasheet_hiseq_systems.pdf
+
+ A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word HiSeq.
+ 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.
+ PERSON: Mark Andrew Miller
+ HiSeq series
+ PERSON: Mark Andrew Miller
+ https://github.com/obi-ontology/obi/issues/1825
+ Alicia Clum
+ Illumina HiSeq Series Instrument
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Illumina NextSeq Series Instrument
+ https://www.cd-genomics.com/blog/nextseq/
+
+ A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NextSeq.
+ 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.
+ PERSON: Mark Andrew Miller
+ NextSeq series
+ PERSON: Mark Andrew Miller
+ https://github.com/obi-ontology/obi/issues/1825
+ Alicia Clum
+ Illumina NextSeq Series Instrument
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Illumina NovaSeq Series Instrument
+
+ A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NovaSeq.
+ 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.
+ PERSON: Mark Andrew Miller
+ NovaSeq series
+ PERSON: Mark Andrew Miller
+ https://github.com/obi-ontology/obi/issues/1825
+ Alicia Clum
+ Illumina NovaSeq Series Instrument
+
+
+
+
diff --git a/views/NIAID-GSC-BRC.owl b/views/NIAID-GSC-BRC.owl
index ba8e11f1..1f196382 100644
--- a/views/NIAID-GSC-BRC.owl
+++ b/views/NIAID-GSC-BRC.owl
@@ -11,7 +11,7 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#">
-
+
en
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Alan Ruttenberg
@@ -77,7 +77,7 @@
http://creativecommons.org/licenses/by/4.0/
Ontology for Biomedical Investigations
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
- 2024-10-03
+ 2024-10-25
diff --git a/views/obi.obo b/views/obi.obo
index a2f257e1..161f0f10 100644
--- a/views/obi.obo
+++ b/views/obi.obo
@@ -1,6 +1,6 @@
format-version: 1.2
-data-version: 2024-10-03
-date: 03:10:2024 14:53
+data-version: 2024-10-25
+date: 25:10:2024 12:39
synonymtypedef: OMO:0003000 "abbreviation"
synonymtypedef: OMO:0003001 "ambiguous synonym"
synonymtypedef: OMO:0003002 "dubious synonym"
@@ -80,7 +80,7 @@ property_value: http://purl.org/dc/elements/1.1/subject "An ontology for the ann
property_value: http://purl.org/dc/terms/license "http://creativecommons.org/licenses/by/4.0/" xsd:string
property_value: http://purl.org/dc/terms/title "Ontology for Biomedical Investigations" xsd:string
property_value: IAO:0000589 "Ontology for Biomedical Investigations" xsd:string
-property_value: owl:versionInfo "2024-10-03" xsd:string
+property_value: owl:versionInfo "2024-10-25" xsd:string
[Term]
id: BFO:0000001
@@ -14798,10 +14798,10 @@ is_a: OBI:0003128 ! T cell epitope assay
[Term]
id: OBI:0002000
-name: Genome Analyzer IIx
+name: Illumina Genome Analyzer IIx
def: "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." []
+synonym: "Genome Analyzer IIx" EXACT []
synonym: "Illumina GA IIx" EXACT []
-synonym: "Illumina Genome Analyzer IIx" EXACT []
is_a: OBI:0000703 ! Illumina Genome Analyzer II
[Term]
@@ -14809,20 +14809,20 @@ id: OBI:0002001
name: Illumina HiSeq 2000
def: "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." []
synonym: "HiSeq 2000" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003683 ! Illumina HiSeq Series Instrument
[Term]
id: OBI:0002002
name: Illumina HiSeq 2500
def: "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." []
synonym: "HiSeq 2500" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003683 ! Illumina HiSeq Series Instrument
[Term]
id: OBI:0002003
-name: MiSeq
+name: Illumina MiSeq
def: "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." []
-synonym: "Illumina MiSeq" EXACT []
+synonym: "MiSeq" EXACT []
is_a: OBI:0400103 ! DNA sequencer
[Term]
@@ -14951,17 +14951,17 @@ is_a: OBI:0000070 ! assay
[Term]
id: OBI:0002021
-name: NextSeq 500
+name: Illumina NextSeq 500
def: "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology." []
-synonym: "Illumina NextSeq 500" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+synonym: "NextSeq 500" EXACT []
+is_a: OBI:0003684 ! Illumina NextSeq Series Instrument
[Term]
id: OBI:0002022
name: Illumina HiSeq 1000
def: "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology." []
synonym: "HiSeq 1000" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003683 ! Illumina HiSeq Series Instrument
[Term]
id: OBI:0002023
@@ -15000,10 +15000,10 @@ is_a: OBI:0001307 ! tiling microarray
[Term]
id: OBI:0002027
-name: Genome Analyzer IIe
+name: Illumina Genome Analyzer IIe
def: "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 IIe makes industry-leading next-generation sequencing technology accessible to more laboratories." []
+synonym: "Genome Analyzer IIe" EXACT []
synonym: "Illumina GA IIe" EXACT []
-synonym: "Illumina Genome Analyzer IIe" EXACT []
is_a: OBI:0000703 ! Illumina Genome Analyzer II
[Term]
@@ -15166,14 +15166,14 @@ id: OBI:0002048
name: Illumina HiSeq 3000
def: "A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day." []
synonym: "HiSeq 3000" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003683 ! Illumina HiSeq Series Instrument
[Term]
id: OBI:0002049
name: Illumina HiSeq 4000
def: "A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day." []
synonym: "HiSeq 4000" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003683 ! Illumina HiSeq Series Instrument
[Term]
id: OBI:0002050
@@ -15748,7 +15748,7 @@ id: OBI:0002129
name: Illumina HiSeq X Ten
def: "A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems." []
synonym: "HiSeq X Ten" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003683 ! Illumina HiSeq Series Instrument
[Term]
id: OBI:0002130
@@ -17983,7 +17983,7 @@ id: OBI:0002630
name: Illumina NovaSeq 6000
def: "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters." []
synonym: "NovaSeq 6000" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003685 ! Illumina NovaSeq Series Instrument
[Term]
id: OBI:0002631
@@ -22272,13 +22272,13 @@ id: OBI:0003386
name: Illumina HiSeq 1500
def: "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option." []
synonym: "HiSeq 1500" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003683 ! Illumina HiSeq Series Instrument
[Term]
id: OBI:0003387
-name: NextSeq 550
+name: Illumina NextSeq 550
def: "A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing." []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003684 ! Illumina NextSeq Series Instrument
[Term]
id: OBI:0003388
@@ -23492,7 +23492,7 @@ id: OBI:0003606
name: Illumina NextSeq 1000
def: "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells." []
synonym: "NextSeq 1000" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003684 ! Illumina NextSeq Series Instrument
[Term]
id: OBI:0003607
@@ -23842,7 +23842,7 @@ name: Illumina NovaSeq X
def: "A DNA sequencer with three flow cell types manufactured by Illumina. The NovaSeq X provides an output of up to 8 Tb (26-52 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing." []
synonym: "NovaSeq X Series" EXACT []
synonym: "NovaSeq X System" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003685 ! Illumina NovaSeq Series Instrument
[Term]
id: OBI:0003664
@@ -23850,7 +23850,7 @@ name: Illumina NovaSeq X Plus
def: "A DNA sequencer with three flow cell types manufactured by Illumina. It features a dual-flow cell configuration, allowing to reach an output of up to 16 Tb (52-104 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing." []
synonym: "NovaSeq X Series" EXACT []
synonym: "NovaSeq X System" EXACT []
-is_a: OBI:0400103 ! DNA sequencer
+is_a: OBI:0003685 ! Illumina NovaSeq Series Instrument
[Term]
id: OBI:0003666
@@ -23865,6 +23865,27 @@ def: "A specimen collected through oral cavity lavage that contains the reagents
synonym: "mouth rinse specimen" EXACT []
is_a: OBI:0003666 ! lavage fluid specimen
+[Term]
+id: OBI:0003683
+name: Illumina HiSeq Series Instrument
+def: "A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word HiSeq." []
+synonym: "HiSeq series" EXACT []
+is_a: OBI:0400103 ! DNA sequencer
+
+[Term]
+id: OBI:0003684
+name: Illumina NextSeq Series Instrument
+def: "A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NextSeq." []
+synonym: "NextSeq series" EXACT []
+is_a: OBI:0400103 ! DNA sequencer
+
+[Term]
+id: OBI:0003685
+name: Illumina NovaSeq Series Instrument
+def: "A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NovaSeq." []
+synonym: "NovaSeq series" EXACT []
+is_a: OBI:0400103 ! DNA sequencer
+
[Term]
id: OBI:0005246
name: injection function
diff --git a/views/obi_core.owl b/views/obi_core.owl
index 84b9f173..03bd7c4e 100644
--- a/views/obi_core.owl
+++ b/views/obi_core.owl
@@ -11,7 +11,7 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#">
-
+
en
Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
@@ -78,7 +78,7 @@
http://creativecommons.org/licenses/by/4.0/
Ontology for Biomedical Investigations
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
- 2024-10-03
+ 2024-10-25