/usr/lib/R/site-library/AnnotationDbi/DBschemas/schemas_0.9/DataTypes.txt is in r-bioc-annotationdbi 1.26.1-1.
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--------------
SQL type: VARCHAR(10)
Examples: '10251', '283297', '100113407'
Note: highest value observed so far is 100113407
manufacturer ID
---------------
SQL type: VARCHAR(80)
Examples: '1000_at', '1002_f_at', 'AFFX-HUMISGF3A/M97935_MA_at'
GenBank accession number
------------------------
SQL type: VARCHAR(20)
Examples: 'X60188', 'NR_003589', 'HG3432-HT3618'
Note: the maximum length observed so far is 13 but using VARCHAR(20)
is a safety precaution for longer accession numbers that could
appear in the future
gene symbol or alias
--------------------
SQL type: VARCHAR(80)
Examples: 'NPEPPS', 'myr4', 'DKFZp434G0625PRO34003'
Note: the maximum length observed so far is 21 but using VARCHAR(80)
is a safety precaution for longer aliases that could appear in
the future
sequence name
-------------
SQL type: VARCHAR(20)
Examples: '1', '22', 'X', 'Y', '6_cox_hap1', '22_random'
chromosome name
---------------
SQL type: VARCHAR(2)
Examples: '1', '22', 'X', 'Y', 'M', 'MT', 'Un'
Note: a chromosome name is a particular sequence name
cytoband location
-----------------
SQL type: VARCHAR(20)
Examples: '1p34.2', 'Yp11.32', '19q13.11-q13.12'
Note: the maximum length observed so far is 15 but using VARCHAR(20)
is a safety precaution for longer cytoband locations that could
appear in the future
EC number (no "EC:" prefix)
---------------------------
SQL type: VARCHAR(13)
Examples: '1.1.4.1', '3.2.1.14', '1.14.99.36'
Note: the maximum length observed so far is 10 but using VARCHAR(13)
is a safety precaution for longer EC numbers that could
appear in the future
EC number (with "EC:" prefix)
-----------------------------
SQL type: VARCHAR(16)
Examples: 'EC:1.1.4.1', 'EC:3.2.1.14', 'EC:1.14.99.36'
EC name
-------
SQL type: VARCHAR(255)
Examples: 'lipase', 'photosystem I', '6-phosphofructokinase'
Note: the maximum length observed so far is 99
gene name
---------
SQL type: VARCHAR(255)
Examples: 'deoxyribonuclease I-like 1', 'vitrin'
Note: the maximum length observed so far is 251
OMIM ID
-------
SQL type: CHAR(6)
Examples: '231550', '601421', '611258'
Note: highest value observed so far is 611258
IPI accession number
--------------------
SQL type: CHAR(11)
Examples: 'IPI00328276', 'IPI00789644'
Pfam ID
-------
SQL type: CHAR(7)
Examples: 'PF00069', 'PF08266'
PROSITE ID
----------
SQL type: CHAR(7)
Examples: 'PS00107', 'PS00657'
PubMed ID
---------
SQL type: VARCHAR(10)
Examples: '2437', '2583089', '17652175'
Note: highest value observed so far is 17652175
RefSeq accession number
-----------------------
SQL type: VARCHAR(20)
Examples: 'NM_018009', 'NP_001035700'
Note: RefSeq accession numbers seem to be valid GenBank accession numbers
UniGene ID
----------
SQL type: VARCHAR(10)
Examples: 'Hs.2', 'Hs.511848', 'Hs.695912'
Note: highest value observed so far for Human is Hs.695912
FlyBase ID
----------
SQL type: CHAR(11)
Examples: 'FBgn0001942', 'FBgn0030936', 'FBgn0051992'
Yeast ORF ID
------------
SQL type: VARCHAR(14)
Examples: 'YPL141C', 'YGRWsigma7', 'YPRWdelta14'
Note: the maximum length observed so far is 11 but using VARCHAR(14)
is a safety precaution for longer Yeast ORF IDs
that could appear in the future
Yeast gene name
---------------
SQL type: VARCHAR(14)
Examples: 'ADK2', 'TMA23', '21S_RRNA_4', 'MF(ALPHA)1'
Note: the maximum length observed so far is 10 but using VARCHAR(14)
is a safety precaution for longer Yeast gene names
that could appear in the future
SGD ID
------
SQL type: CHAR(10)
Examples: 'S000004794', 'S000037040', 'S000123281'
Note: highest value observed so far is S000123281
Yeast feature description
-------------------------
SQL type: TEXT
Note: this can be a text of any length
Yeast gene alias
----------------
SQL type: VARCHAR(13)
Examples: 'CDH1', 'DNA33', 'EF-1 alpha', 'ATPEPSILON'
Note: the maximum length observed so far is 10 but using VARCHAR(13)
is a safety precaution for longer Yeast gene aliases that could
appear in the future
InterPro ID
-----------
SQL type: CHAR(9)
Examples: 'IPR001440', 'IPR008688', 'IPR015809'
Note: highest value observed so far is IPR015809
SMART ID
--------
SQL type: CHAR(7)
Examples: 'SM00055', 'SM00220', 'SM00717'
AGI locus ID
------------
SQL type: CHAR(9)
Examples: 'AT1G01010', 'ATCG00830', 'ATMG01410'
AraCyc pathway name
-------------------
SQL type: VARCHAR(255)
Examples: 'SAM cycle', 'trans,trans-farnesyl diphosphate biosynthesis'
Note: the maximum length observed so far is 77 but using VARCHAR(255)
is a safety precaution for longer AraCyc pathways that could appear
in the future
Arabidopsis chromosome
----------------------
SQL type: CHAR(1)
7 possible values: '1', '2', '3', '4', '5', 'C', 'M'
GO ontology (short label)
-------------------------
SQL type: VARCHAR(9)
4 possible values: 'universal', 'BP', 'CC', 'MF'
GO ontology (full label)
------------------------
SQL type: VARCHAR(18)
4 possible values: 'universal', 'biological_process', 'cellular_component',
'molecular_function'
GO ID
-----
SQL type: CHAR(10)
Examples: 'all', 'GO:0000001', 'GO:0016491'
Note: except for 'all' they are all of the form 'GO:1234567'
textual label for the GO term
-----------------------------
SQL type: VARCHAR(255)
Examples: 'larval fat body development',
'age-dependent response to reactive oxygen species during chronological cell aging'
Note: the maximum length observed so far is 193
textual definition for the GO term
----------------------------------
SQL type: TEXT
Note: this can be a text of any length
type of GO child-parent relationship
------------------------------------
SQL type: VARCHAR(7)
2 possible values: 'isa', 'part_of'
GO evidence code
----------------
SQL type: CHAR(3)
14 possible values: 'IC', 'IDA', 'IEA', 'IEP', 'IGC', 'IGI', 'IMP', 'IPI',
'ISS', 'NAS', 'ND', 'RCA', 'TAS', 'NR'
Note: see http://www.geneontology.org/GO.evidence.shtml
for the meaning of the GO evidence codes
KEGG pathway short ID
---------------------
SQL type: CHAR(5)
Examples: '00100', '05223', '07218'
Note: highest value observed so far is 07218
KEGG pathway long ID
--------------------
SQL type: CHAR(8)
Examples: 'hsa00680', 'rno05220', 'ath00120', 'dme00910'
KEGG pathway name
-----------------
SQL type: VARCHAR(80)
Examples: 'Butanoate metabolism', '3-Chloroacrylic acid degradation'
Note: the maximum length observed so far is 63
Entrez Gene or ORF ID
---------------------
SQL type: VARCHAR(20)
Examples: 'YDR156W', 'AT4G15280', 'Dmel_CG10045' or an Entrez Gene ID
Note: the maximum length observed so far is 12
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