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The Ontology for Biomedical Investigations
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Material type related terms needed by MO #480

Closed obi-bot closed 7 years ago

obi-bot commented 14 years ago

Driving use cases of the MGED ontology (MO) is MAGE-TAB files.

MAGE-TAB format files are simple tab-delimited spreadsheet files (SDRF file is one type of MAGE-TAB files) used to describe a microarray experiment. They typically contain some annotations using the MO.

Material type related terms are used in MAGE-TAB files to describe the state of biomaterial during the process of a microarray experiment, can be applied to other kinds of experiments.

Definition of MaterialType in MO: Controlled terms for the state of the BioMaterial. Each state (BioSource, different BioSamples, and LabeledExtract) have MaterialTypes. Examples are population of an organism, organism, organism part, cell, etc.

The following 11 MaterialType related terms are requested to be added to OBI under "material_entity". Most of these terms are processed material. - cell_lysate - cytoplasmic_RNA - genomic_DNA - molecular_mixture - nuclear_RNA - organellar_RNA - polyA_RNA - synthetic_DNA - synthetic_RNA - total_RNA - whole_organism

MaterialType related MO terms used in MAGE-TAB SDRF files: - cell_lysate MO definition: a collection of cells whose membranes have been disrupted. - cytoplasmic_RNA MO definition: RNA obtained from the cytoplasm. - genomic_DNA MO definition: high molecular weight DNA - molecular_mixture MO definition: an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins - nuclear_RNA MO definition: RNA obtained from the nucleus. - organellar_RNA MO definition: RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus. - polyA_RNA MO definition: RNA which has been obtained by selection for polyA tracts. Exact synonym: polyA+_RNA, Non-exact synonym: mRNA - synthetic_DNA MO definition: DNA which is generated by chemical or enzymatic (non cellular) means. non-exact synonym: cDNA - synthetic_RNA MO definition: RNA which is generated by chemical or enzymatic (non cellular) means. E.g. T7 promotor generated RNA. Non-exact synonym: cRNA, complementary RNA aRNA, amplified RNA - total_RNA MO definition: Total cellular and nuclear RNA. - whole_organism MO definition: one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria - DNA (mapped to CHEBI#CHEBI_16991 deoxyribonucleic acids) MO definition: Deoxyribonucleic acid. - cell (mapped to CL#CL_0000000 cell) MO definition: One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms. - organism_part (mapped to OBI_0100015 anatomical entity) MO definition: The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).

USE CASES

Use case 1: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-CBIL-13 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-CBIL-13/E-CBIL-13.sdrf.txt Used terms: synthetic_RNA, DNA

Use case 2: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-GEOD-2555 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-2555/E-GEOD-2555.sdrf.txt Used terms: cell, total_RNA

Use case 3: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MAXD-17 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-MAXD-17/E-MAXD-17.sdrf.txt Used terms: cell, synthetic_RNA

Use case 4: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-SGRP-1 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-SGRP-1/E-SGRP-1.sdrf.txt Used terms: cell_lysate, DNA

Use case 5: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-WMIT-1 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-WMIT-1/E-WMIT-1.sdrf.txt Used terms: cell_lysate

Use case 6: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-GEOD-8646 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-8646/E-GEOD-8646.sdrf.txt Used terms: cytoplasmic_RNA, synthetic_RNA

Use case 7: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-BUGS-29 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-BUGS-29/E-BUGS-29.sdrf.txt Used terms: genomic_DNA, synthetic_DNA

Use case 8: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-TABM-10 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-TABM-10/E-TABM-10.sdrf.txt Used terms: genomic_DNA

Use case 9: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MAXD-48 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-MAXD-48/E-MAXD-48.sdrf.txt Used terms: molecular_mixture, DNA

Use case 10: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-GEOD-2817 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-2817/E-GEOD-2817.sdrf.txt Used terms: nuclear_RNA, total_RNA, synthetic_RNA

Use case 11: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-GEOD-4975 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-4975/E-GEOD-4975.sdrf.txt Used terms: polyA_RNA, synthetic_RNA

Use case 12: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MEXP-282 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-282/E-MEXP-282.sdrf.txt Used terms: organellar_RNA

Use case 13: Experiments: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-GEOD-11974 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-11974/E-GEOD-11974.sdrf.txt Used terms: whole_organism, organism_part, total_RNA, synthetic_RNA

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Reported by: zhengj2007

Original Ticket: obi/obi-terms/488

obi-bot commented 14 years ago

In these examples, the material types are used to specify the inputs and outputs of protocols (processes). All the requested terms can be defined as an output of some material transformation except for whole organism. Some of these can also be defined in a general sense such as nuclear RNA.

Original comment by: cstoeckert

obi-bot commented 14 years ago

cell_lysate - OBI_1000036 cell lysate

genomic_DNA - add to OBI on Dec 17, Dev call named as "high molecular weight DNA extract"

Original comment by: zhengj2007

obi-bot commented 14 years ago

Jie - I am unsure what is the status on those. There is no assignee, and is there something preventing you from adding those as needed? Thanks, Melanie

Original comment by: mcourtot

obi-bot commented 14 years ago

All these material type terms (except whole_organism) are processed material, the specific output of a planned process.

We are focusing on the terms which are the output of a RNA extraction process. total_RNA polyA_RNA cytoplasmic_RNA nuclear_RNA organellar_RNA

Chris and I defined the design pattern for these terms are: All the RNA extract material entities are the specified output of a RNA extraction process. Since the MO term labels are not appropriate, we renamed them. Details please check the attached file (materialType.xls). We also provide textual definition and example of usage of the terms.

Besides, we request to add more specified input and output to the following extraction processes.

OBI_0666667 Nucleic acid extraction 'has_specified_input' some 'sample from organism' or 'organism' or 'cell culture' 'has_specified_output' some 'nucleic acid'

OBI_0000257 DNA extraction 'has_specified_output' some 'deoxyribonucleic acid'

OBI_0666666 RNA extraction 'has_specified_output' some 'ribonucleic acid'

Original comment by: zhengj2007

obi-bot commented 14 years ago

Dev call Jan 25, 2010

OK with the Pattern of RNA related terms submitted by Chris and Jie in the spreadsheet format. AI: JZ will add the terms based on the submitted spreadsheet file into OBI. AI: CS and JZ will work on the rest of Material type MO terms using the same way.

Original comment by: zhengj2007

obi-bot commented 14 years ago

RNA extract/extraction terms (with restrictions)

Original comment by: zhengj2007

obi-bot commented 14 years ago

Terms and some restrictions were added according to the speadsheet: https://sourceforge.net/tracker/download.php?group\_id=177891&atid=886178&file\_id=360446&aid=2915152

Original comment by: zhengj2007

obi-bot commented 14 years ago

By checking the use cases, most of synthetic_RNA and synthetic_DNA were used as the output of a labeling process.

So suggest add two terms: labeled RNA labeled DNA as the subclasses of material entity with restriction is specified output of some 'labeling' (OBI_0600038)

There is OBI_0000839 labeled oligonucleotide. We may split the term to labeled oligo DNA and labeled oligo RNA and add them as the subclass of labeled DNA and labeled RNA.

Original comment by: zhengj2007

obi-bot commented 14 years ago

Original comment by: zhengj2007

obi-bot commented 8 years ago

Original comment by: zhengj2007

obi-bot commented 8 years ago

terms were added.

Original comment by: zhengj2007