r-bioc-annotationdbi 1.26.1-1 / usr / lib / R / site-library / AnnotationDbi / DBschemas / schemas_2.1 / DataTypes.txt

AC ID
--------------
  SQL type: VARCHAR(12)
  Examples: 'PF00389.21', 'PF02826.10', 'P63103.1'
  Note: max length appears to be about 10 This seems to be the central ID for all things PFAM.

CAZY ID
--------------
  SQL type: VARCHAR(6)
  Examples: 'GT_57', 'GH_29', 'CBM_19'
  Note: max length seems to be 6

HOMSTRAD ID
--------------
  SQL type: VARCHAR(20)
  Examples: 'Dala_Dala_ligas_N', 'A2M_B', 'Haloperoxidase'
  Note: max length seems to be less than 20

INTERPRO ID
--------------
  SQL type: VARCHAR(9)
  Examples: 'IPR003391', 'IPR002612', 'IPR005830'
  Note: max length seems to be 9

LOAD ID 
--------------
  SQL type: VARCHAR(15)
  Examples: 'Adrenomedullin', 'Adeno_PIX', 'BCMA-Tall_bind'
  Note: max length seems to be less than 15

MEROPS ID
--------------
  SQL type: VARCHAR(3)
  Examples: 'S10', 'M55', 'T1'
  Note: max length seems to be 3

MIM ID
--------------
  SQL type: VARCHAR(6)
  Examples: '104311', '128230', '222600'
  Note: max length seems to be 6

PDB ID
--------------
  SQL type: VARCHAR(6)
  Examples: '1u69 B', '1odn A', '2kfn A'
  Note: max length seems to be 6

start of alignment
--------------
  SQL type: INTEGER
  Examples: '3', '180', '256'
  Note: just an int

end of alignment
--------------
  SQL type: INTEGER
  Examples: '288', '224', '334'
  Note: always just an int

PFAMB ID
--------------
  SQL type: VARCHAR(8)
  Examples: 'PB012689', 'PB177858', 'PB176422'
  Note: max length seems to be 8, these are the machine called PFAM IDs.

PRINTS ID
--------------
  SQL type: VARCHAR(7)
  Examples: 'PR00178', 'PR01233', 'PR00543'
  Note: max length seems to be 7

PROSITE ID
--------------
  SQL type: VARCHAR(9)
  Examples: 'PDOC00403', 'PDOC00174', 'PDOC00578'
  Note: max length seems to be 9

PROSITE_PROFILE ID
--------------
  SQL type: VARCHAR(7)
  Examples: 'PS50032', 'PS50203', 'PS50119'
  Note: max length seems to be 7

RM ID
--------------
  SQL type: VARCHAR(8)
  Examples: '11011151', '2254264', '15531590'
  Note: max length seems to be 8

SCOP ID
--------------
  SQL type: VARCHAR(4)
  Examples: '1rla', '1by6', '3gcc'
  Note: max length seems to be 4

SCOP placement
--------------
  SQL type: VARCHAR(2)
  Examples: 'fa', 'fa', 'sf'
  Note: max length seems to be 2. I only ever see the values fa and sf.

SMART ID
--------------
  SQL type: VARCHAR(9)
  Examples: 'ZnF_UBR1', 'RasGEFN', 'PLDc'
  Note: max length seems to be about 9

TC ID
--------------
  SQL type: VARCHAR(6)
  Examples: '3.A.15', '9.B.33', '2.A.27'
  Note: max length seems to be 

PFAM ID ID
--------------
  SQL type: VARCHAR(15)
  Examples: 'ADP_ribosyl_GH', 'Adeno_E1B_55K_N', 'AfaD'
  Note: max length seems to be 15

DE ID
--------------
  SQL type: VARCHAR(80)
  Examples: 'Adenovirus GP19K', 'ADP-specific Phosphofructokinase/Glucokinase conserved region'
  Note: A description field.  This one can be very big

TP ID
--------------
  SQL type: VARCHAR(6)
  Examples: 'Repeat', 'Family', 'Domain', 'Motif'
  Note: max length is 6.  This is only ever one of the above 4 values.

URL ID
--------------
  SQL type: VARCHAR(80)
  Examples: 'http://bioinformatics.weizmann.ac.il/hotmolecbase/entries/ps1.htm'
  Note: max length is unknown.  These can obviously get pretty big.


Inparanoid ID
--------------
  SQL type: VARCHAR(30)
  Examples: 'ENSP00000351750', 'FBpp0073215', 'MGI:1274784'
  Note: character string that corresponds to a gene OR protein ID.  IDs from one species are all of the same type, but what type will be used for a species can vary...

Inparanoid Cluster ID
--------------
  SQL type: INTEGER
  Examples: '1', '2', '34'
  Note: These are integers which indicate the groupings assigned by inparanoids algorithm.

Inparanoid Species ID
--------------
  SQL type: VARCHAR(15)
  Examples: 'ensHOMSA.fa', 'modMUSMU.fa', 'modDROME.fa'
  Note: These indicate the species, the type of ID used by Inparanoid ID and finally the kind of table these data were extracted from

Inparanoid Score
--------------
  SQL type: VARCHAR(20)
  Examples: '1.0', '0.1513', '0.3578'
  Note: The score indicates the degree to which this protein is considered to belong to the Inparanoid grouping 

Inparanoid Seed Status
--------------
  SQL type: VARCHAR(4)
  Examples: '100%', '', '99%'
  Note: 0 to 100%.  100% indicates a true "seed" paralog.

Entrez Gene ID
--------------
  SQL type: VARCHAR(10)
  Examples: '10251', '283297', '100113407'
  Note: highest value observed so far is 100113407

Ensembl Gene ID
--------------
  SQL type: VARCHAR(20)
  Examples: 'ENSRNOG00000016924', 'ENSMUSG00000028125', 'ENSG00000127837'
  Note: highest value observed so far is 18 characters long

Ensembl Protein ID
--------------
  SQL type: VARCHAR(20)
  Examples: 'ENSP00000370606', 'ENSRNOP00000027'
  Note: Ensembl protein IDs, one peptide per ID.

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'

FlyBase CG ID
----------
  SQL type: CHAR(10)
  Examples: 'CG3038', 'CG13377', 'CG2945'

Flybase Protein ID
--------------
  SQL type: VARCHAR(20)
  Examples: 'FBpp0073215', 'FBpp0110310', 'FBpp0071474'
  Note: Flybase protein IDs, one peptide per ID.

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