Handling Synopsis Lists
From LipidomicsWiki
Contents |
Current Handling / Status
The Synopsis list
For the moment, our Synopsis is hold as an excel list.
Structure of the synopsis (excel)
The synopsis consists of an excel-sheet with the following columns:
1 | ID | a unique counter for every gene and headline |
2 | Pathway | a number for the pathway the headline or gene in this row belongs to (actually 1-78) |
3 | LfdNr | a counter within every pathway for every gene and sub-headline |
4 | Unigene | The Unigene-ID of the gene in this row. 0 for Headlines and sub-headlines |
5 | Title | The Name of the gene or headline |
6 | Symbol | The HGNC symbol for the gene in this row. Empty for headlines |
7 | ChromLoc | The chromosomal locus for the gene in this row. Empty for headlines |
8 | EnsEMBL Gene ID | The ENSG... for the gene in this row. 0 for headlines |
And here as an example some short parts of the synopsis:
ID | Pathway | LfdNr | Unigene | Title | Symbol | ChromLoc | Ensembl Gene ID |
1 | 1 | 1 | 0 | Stem Cell differentiation (WNT,Notch,HOX,FOXO) | 0 | ||
2 | 1 | 2 | 0 | WNT | 0 | ||
3 | 1 | 3 | Hs.248164 | wingless-type MMTV integration site family, member 1 | WNT1 | 12q13 | ENSG00000125084 |
4 | 1 | 4 | Hs.567356 | wingless-type MMTV integration site family member 2 | WNT2 | 7q31 | ENSG00000105989 |
5 | 1 | 5 | Hs.258575 | wingless-type MMTV integration site family, member 2B | WNT2B | 1p13 | ENSG00000134245 |
6 | 1 | 6 | Hs.445884 | wingless-type MMTV integration site family, member 3 | WNT3 | 17q21 | ENSG00000108379 |
7 | 1 | 7 | Hs.336930 | wingless-type MMTV integration site family, member 3A | NOC | ||
8 | 1 | 8 | Hs.25766 | CDNA clone IMAGE:3690160 | WNT4 | 01p36.23-p35.1 | ENSG00000162552 |
9 | 1 | 9 | Hs.152213 | Transcribed locus, strongly similar to NP_003383.2 wingless-type MMTV integration site family, member 5A precursor | WNT5A | 03p21-p14 | ENSG00000114251 |
10 | 1 | 10 | Hs.306051 | Wingless-type MMTV integration site family, member 5B | WNT5B | 12p13.3 | ENSG00000111186 |
11 | 1 | 11 | Hs.29764 | wingless-type MMTV integration site family, member 6 | WNT6 | 2q35 | ENSG00000115596 |
12 | 1 | 12 | Hs.72290 | wingless-type MMTV integration site family, member 7A | WNT7A | 3p25 | ENSG00000154764 |
13 | 1 | 13 | Hs.591274 | wingless-type MMTV integration site family, member 8A | WNT8A | 5q31 | ENSG00000061492 |
14 | 1 | 14 | Hs.421281 | wingless-type MMTV integration site family, member 8B | WNT8B | 10q24 | ENSG00000075290 |
15 | 1 | 15 | Hs.149504 | Wingless-type MMTV integration site family, member 9A | WNT9A | 1q42 | ENSG00000143816 |
16 | 1 | 16 | Hs.326420 | wingless-type MMTV integration site family, member 9B | WNT9B | 17q21 | ENSG00000158955 |
17 | 1 | 17 | Hs.121540 | wingless-type MMTV integration site family, member 10A | WNT10A | 2q35 | ENSG00000135925 |
18 | 1 | 18 | Hs.91985 | wingless-type MMTV integration site family, member 10B | WNT10B | 12q13 | ENSG00000169884 |
19 | 1 | 19 | Hs.108219 | wingless-type MMTV integration site family, member 11 | WNT11 | 11q13.5 | ENSG00000085741 |
20 | 1 | 20 | Hs.272375 | wingless-type MMTV integration site family, member 16 | WNT16 | 7q31 | ENSG00000002745 |
21 | 1 | 21 | Hs.592145 | WNT1 inducible signaling pathway protein 2 | WISP2 | 20q12-q13.1 | ENSG00000064205 |
22 | 1 | 22 | Hs.558428 | WNT1 inducible signaling pathway protein 3 | WISP3 | 6q21 | ENSG00000112761 |
23 | 1 | 23 | 0 | Frizzled | 0 | ||
24 | 1 | 24 | Hs.94234 | frizzled homolog 1 (Drosophila) | FZD1 | 7q21 | ENSG00000157240 |
25 | 1 | 25 | Hs.142912 | frizzled homolog 2 (Drosophila) | FZD2 | 17q21.1 | ENSG00000180340 |
26 | 1 | 26 | Hs.40735 | frizzled homolog 3 (Drosophila) | FZD3 | 8p21 | ENSG00000104290 |
27 | 1 | 27 | Hs.591968 | frizzled homolog 4 (Drosophila) | FZD4 | 11q14.2 | ENSG00000174804 |
28 | 1 | 28 | frizzled homolog 5 (Drosophila) | FZD5 | ENSG00000163251 | ||
29 | 1 | 29 | Hs.591863 | frizzled homolog 6 (Drosophila) | FZD6 | 8q22.3-q23.1 | ENSG00000164930 |
30 | 1 | 30 | Hs.173859 | frizzled homolog 7 (Drosophila) | FZD7 | 2q33 | ENSG00000155760 |
31 | 1 | 31 | Hs.302634 | frizzled homolog 8 (Drosophila) | FZD8 | 10p11.21 | ENSG00000177283 |
32 | 1 | 32 | Hs.534367 | frizzled homolog 9 (Drosophila) | FZD9 | 7q11.23 | ENSG00000188763 |
33 | 1 | 33 | Hs.31664 | frizzled homolog 10 (Drosophila) | FZD10 | 12q24.33 | ENSG00000111432 |
34 | 1 | 34 | Hs.437846 | smoothened homolog (Drosophila) | SMO | 7q32.3 | ENSG00000128602 |
35 | 1 | 35 | 0 | Frizzled interacting with Wnt | 0 | ||
36 | 1 | 36 | Hs.213424 | secreted frizzled-related protein 1 | SFRP1 | 8p12-p11.1 | ENSG00000104332 |
37 | 1 | 37 | Hs.481022 | secreted frizzled-related protein 2 | SFRP2 | 4q31.3 | ENSG00000145423 |
38 | 1 | 38 | Hs.128453 | Frizzled-related protein | FRZB | 2qter | ENSG00000162998 |
39 | 1 | 39 | Hs.416007 | secreted frizzled-related protein 4 | SFRP4 | 7p14.1 | ENSG00000106483 |
40 | 1 | 40 | Hs.279565 | secreted frizzled-related protein 5 | SFRP5 | 10q24.1 | ENSG00000120057 |
41 | 1 | 41 | Hs.558009 | secreted and transmembrane 1 | SECTM1 | 17q25 | ENSG00000141574 |
42 | 1 | 42 | 0 | LRPs | 0 | ||
43 | 1 | 43 | Hs.162757 | low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor) | LRP1 | 12q13-q14 | ENSG00000123384 |
44 | 1 | 44 | Hs.470117 | low density lipoprotein-related protein 1B (deleted in tumors) | LRP1B | 2q21.2 | ENSG00000168702 |
45 | 1 | 45 | Hs.470538 | low density lipoprotein-related protein 2 | LRP2 | 2q24-q31 | ENSG00000081479 |
46 | 1 | 46 | Hs.515340 | low density lipoprotein receptor-related protein 3 | LRP3 | 19q13.11 | ENSG00000130881 |
47 | 1 | 47 | Hs.4930 | Low density lipoprotein receptor-related protein 4 | LRP4 | 11p11.2-p12 | ENSG00000134569 |
48 | 1 | 48 | Hs.6347 | Low density lipoprotein receptor-related protein 5 | LRP5 | 11q13.4 | ENSG00000162337 |
49 | 1 | 49 | Hs.584775 | low density lipoprotein receptor-related protein 6 | LRP6 | 12p11-p13 | ENSG00000070018 |
50 | 1 | 50 | Hs.576154 | low density lipoprotein receptor-related protein 8, apolipoprotein e receptor | LRP8 | 1p34 | ENSG00000157193 |
51 | 1 | 51 | Hs.525232 | low density lipoprotein receptor-related protein 10 | LRP10 | 14q11.2 | ENSG00000197324 |
52 | 1 | 52 | Hs.511818 | retinoic acid early transcript 1E | RAET1E | 6q25.1 | ENSG00000164520 |
53 | 1 | 53 | Hs.517868 | leucine rich repeat containing 3B | LRRC3B | 3p24 | ENSG00000179796 |
54 | 1 | 54 | Hs.502814 | LRP16 protein | LRP16 | 11q11 | |
55 | 1 | 55 | Hs.558513 | LRP2 binding protein | LRP2BP | 4q35.1 | ENSG00000109771 |
994 | 2 | 1 | 0 | EGF-signaling | 0 | ||
995 | 2 | 2 | Hs.419815 | epidermal growth factor (beta-urogastrone) | EGF | 4q25 | ENSG00000138798 |
996 | 2 | 3 | Hs.170009 | transforming growth factor, alpha | TGFA | 2p13 | ENSG00000163235 |
997 | 2 | 4 | Hs.488293 | epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) | EGFR | 7p12 | ENSG00000146648 |
998 | 2 | 5 | Hs.446352 | v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) | ERBB2 | 17q21.1 | ENSG00000141736 |
999 | 2 | 6 | Hs.270833 | Amphiregulin (schwannoma-derived growth factor) | AREG | 4q13-q21 | ENSG00000205595 |
1000 | 2 | 7 | Hs.632601 | amphiregulin (schwannoma-derived growth factor) /// similar to Amphiregulin precursor (AR) (Colorectum cell-derived growth factor) (CRDGF) | AREG /// LOC653193 | 4q13-q21 /// 4q13.3 | |
1001 | 2 | 8 | Hs.632601 | Similar to Amphiregulin precursor (AR) (Colorectum cell-derived growth factor) (CRDGF) | LOC653193 | 4q13.3 | |
1002 | 2 | 9 | Hs.118681 | v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) | ERBB3 | 12q13 | ENSG00000065361 |
1003 | 2 | 10 | Hs.115263 | epiregulin | EREG | 4q13.3 | ENSG00000124882 |
1004 | 2 | 11 | Hs.390729 | v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) | ERBB4 | 2q33.3-q34 | ENSG00000178568 |
1005 | 2 | 12 | Hs.799 | heparin-binding EGF-like growth factor | HBEGF | 5q23 | ENSG00000113070 |
1006 | 2 | 13 | Hs.591704 | betacellulin | BTC | 4q13-q21 | ENSG00000174808 |
1007 | 2 | 14 | Hs.385870 | teratocarcinoma-derived growth factor 1 /// teratocarcinoma-derived growth factor 3, pseudogene | TDGF1 /// TDGF3 | 3p21.31 /// Xq22.3 | |
1008 | 2 | 15 | Hs.503733 | similar to cryptic | LOC653275 | 2q21.1 | |
1009 | 2 | 16 | Hs.567542 | cripto, FRL-1, cryptic family 1 /// similar to cryptic | CFC1 /// LOC653275 | 2q21.1 | |
1010 | 2 | 17 | Hs.453951 | neuregulin 1 | NRG1 | 8p21-p12 | ENSG00000157168 |
1011 | 2 | 18 | Hs.408515 | neuregulin 2 | NRG2 | 5q23-q33 | ENSG00000158458 |
1012 | 2 | 19 | Hs.125119 | neuregulin 3 | NRG3 | 10q22-q23 | ENSG00000185737 |
1013 | 2 | 20 | Hs.238914 | neuregulin 4 | NRG4 | 15q24.2 | ENSG00000169752 |
1014 | 2 | 21 | Hs.591335 | CD164 molecule, sialomucin | CD164 | 6q21 | ENSG00000135535 |
1015 | 2 | 22 | Hs.213289 | low density lipoprotein receptor (familial hypercholesterolemia) | LDLR | 19p13.3 | ENSG00000130164 |
1016 | 2 | 23 | Hs.162757 | low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor) | LRP1 | 12q13-q14 | ENSG00000123384 |
1017 | 2 | 24 | Hs.470117 | low density lipoprotein-related protein 1B (deleted in tumors) | LRP1B | 2q21.2 | ENSG00000168702 |
1018 | 2 | 25 | Hs.470538 | low density lipoprotein-related protein 2 | LRP2 | 2q24-q31 | ENSG00000081479 |
1019 | 2 | 26 | Hs.137572 | rhomboid, veinlet-like 1 (Drosophila) | RHBDL1 | 16p13.3 | ENSG00000103269 |
1020 | 2 | 27 | Hs.524626 | Rhomboid, veinlet-like 2 (Drosophila) | RHBDL2 | 1p34.3 | ENSG00000158315 |
1021 | 2 | 28 | Hs.515340 | low density lipoprotein receptor-related protein 3 | LRP3 | 19q13.11 | ENSG00000130881 |
1022 | 2 | 29 | Hs.591196 | rhomboid, veinlet-like 3 (Drosophila) | RHBDL3 | 17q11.2 | ENSG00000141314 |
1023 | 2 | 30 | Hs.268177 | phospholipase C, gamma 1 /// copine family member IX | PLCG1 /// CPNE9 | 20q12-q13.1 /// 3p25.3 | |
1024 | 2 | 31 | Hs.4930 | Low density lipoprotein receptor-related protein 4 | LRP4 | 11p11.2-p12 | ENSG00000134569 |
1025 | 2 | 32 | Hs.6347 | Low density lipoprotein receptor-related protein 5 | LRP5 | 11q13.4 | ENSG00000162337 |
1026 | 2 | 33 | Hs.413111 | phospholipase C, gamma 2 (phosphatidylinositol-specific) | PLCG2 | 16q24.1 | ENSG00000197943 |
1027 | 2 | 34 | Hs.584775 | low density lipoprotein receptor-related protein 6 | LRP6 | 12p11-p13 | ENSG00000070018 |
1028 | 2 | 35 | Hs.132225 | Phosphoinositide-3-kinase, regulatory subunit 1 (p85 alpha) | PIK3R1 | 5q13.1 | ENSG00000145675 |
1029 | 2 | 36 | Hs.371344 | phosphoinositide-3-kinase, regulatory subunit 2 (p85 beta) | PIK3R2 | 19q13.2-q13.4 | ENSG00000105647 |
1030 | 2 | 37 | Hs.576154 | low density lipoprotein receptor-related protein 8, apolipoprotein e receptor | LRP8 | 1p34 | ENSG00000157193 |
1031 | 2 | 38 | Hs.433795 | SHC (Src homology 2 domain containing) transforming protein 1 | SHC1 | 1q21 | ENSG00000160691 |
1032 | 2 | 39 | Hs.30965 | SHC (Src homology 2 domain containing) transforming protein 2 | SHC2 | 19p13.3 | ENSG00000129946 |
1033 | 2 | 40 | Hs.525232 | low density lipoprotein receptor-related protein 10 | LRP10 | 14q11.2 | ENSG00000197324 |
1034 | 2 | 41 | Hs.137570 | SHC (Src homology 2 domain containing) transforming protein 3 | SHC3 | 9q22.1 | ENSG00000148082 |
1035 | 2 | 42 | Hs.368592 | sortilin-related receptor, L(DLR class) A repeats-containing | SORL1 | 11q23.2-q24.2 | ENSG00000137642 |
1036 | 2 | 43 | Hs.370422 | very low density lipoprotein receptor | VLDLR | 9p24 | ENSG00000147852 |
1037 | 2 | 44 | Hs.591774 | Erbb2 interacting protein | ERBB2IP | 5q12.3 | ENSG00000112851 |
1038 | 2 | 45 | Hs.463928 | discs, large homolog 4 (Drosophila) | DLG4 | 17p13.1 | ENSG00000132535 |
1039 | 2 | 46 | Hs.78824 | tyrosine kinase with immunoglobulin-like and EGF-like domains 1 | TIE1 | 1p34-p33 | ENSG00000066056 |
1040 | 2 | 47 | Hs.444356 | growth factor receptor-bound protein 2 | GRB2 | 17q24-q25 | ENSG00000177885 |
1041 | 2 | 48 | Hs.89640 | TEK tyrosine kinase, endothelial (venous malformations, multiple cutaneous and mucosal) | TEK | 9p21 | ENSG00000120156 |
1042 | 2 | 49 | Hs.234074 | delta-notch-like EGF repeat-containing transmembrane | DNER | ENSG00000187957 | |
1043 | 2 | 50 | Hs.477693 | NCK adaptor protein 1 | NCK1 | 3q21 | ENSG00000158092 |
1044 | 2 | 51 | Hs.529244 | NCK adaptor protein 2 | NCK2 | 2q12 | ENSG00000071051 |
1045 | 2 | 52 | Hs.2375 | egf-like module containing, mucin-like, hormone receptor-like 1 | EMR1 | 19p13.3 | ENSG00000174837 |
1046 | 2 | 53 | Hs.531619 | egf-like module containing, mucin-like, hormone receptor-like 2 | EMR2 | 19p13.1 | ENSG00000127507 |
1047 | 2 | 54 | Hs.461896 | CDNA FLJ38130 fis, clone D6OST2000464 | CRK | 17p13.3 | ENSG00000167193 |
1048 | 2 | 55 | Hs.295626 | integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) | ITGB1 | 10p11.2 | ENSG00000150093 |
1049 | 2 | 56 | Hs.71215 | docking protein 2, 56kDa | DOK2 | 8p21.3 | ENSG00000147443 |
1050 | 2 | 57 | Hs.466039 | CD97 molecule | CD97 | 19p13 | ENSG00000123146 |
1051 | 2 | 58 | Hs.553501 | RAS p21 protein activator (GTPase activating protein) 1 | RASA1 | 5q13.3 | ENSG00000145715 |
1052 | 2 | 59 | Hs.495473 | Notch homolog 1, translocation-associated (Drosophila) | NOTCH1 | 9q34.3 | ENSG00000148400 |
1053 | 2 | 60 | Hs.98445 | RAS p21 protein activator 2 | RASA2 | 3q22-q23 | ENSG00000155903 |
1054 | 2 | 61 | Hs.369188 | RAS p21 protein activator 3 | RASA3 | 13q34 | ENSG00000185989 |
1055 | 2 | 62 | Hs.487360 | Notch homolog 2 (Drosophila) | NOTCH2 | 1p13-p11 | ENSG00000134250 |
1056 | 2 | 63 | Hs.417549 | Protein tyrosine phosphatase, non-receptor type 1 | PTPN1 | 20q13.1-q13.2 | ENSG00000196396 |
1057 | 2 | 64 | Hs.8546 | Notch homolog 3 (Drosophila) | NOTCH3 | 19p13.2-p13.1 | ENSG00000074181 |
1058 | 2 | 65 | Hs.436100 | Notch homolog 4 (Drosophila) | NOTCH4 | 6p21.3 | ENSG00000204301 |
1059 | 2 | 66 | Hs.63489 | protein tyrosine phosphatase, non-receptor type 6 | PTPN6 | 12p13 | ENSG00000111679 |
1060 | 2 | 67 | Hs.195659 | v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) | SRC | 20q12-q13 | ENSG00000197122 |
1061 | 2 | 68 | Hs.379912 | delta-like 1 (Drosophila) | DLL1 | 6q27 | ENSG00000198719 |
1062 | 2 | 69 | Hs.431048 | v-abl Abelson murine leukemia viral oncogene homolog 1 | ABL1 | 9q34.1 | ENSG00000097007 |
1063 | 2 | 70 | Hs.533717 | delta-like 1 homolog (Drosophila) | DLK1 | 14q32 | ENSG00000185559 |
1064 | 2 | 71 | Hs.127792 | Delta-like 3 (Drosophila) | DLL3 | 19q13 | ENSG00000090932 |
1065 | 2 | 72 | Hs.18676 | sprouty homolog 2 (Drosophila) | SPRY2 | 13q31.1 | ENSG00000136158 |
1066 | 2 | 73 | Hs.22140 | cell cycle exit and neuronal differentiation 1 | CEND1 | 11p15.5 | ENSG00000184524 |
1067 | 2 | 74 | Hs.381912 | sprouty homolog 3 (Drosophila) | SPRY3 | ENSG00000168939 | |
1068 | 2 | 75 | Hs.82848 | selectin L (lymphocyte adhesion molecule 1) | SELL | 1q23-q25 | ENSG00000188404 |
1069 | 2 | 76 | Hs.468505 | neurexin 1 | NRXN1 | 2p16.3 | |
1070 | 2 | 77 | Hs.323308 | Sprouty homolog 4 (Drosophila) | SPRY4 | 5q31.3 | ENSG00000187678 |
1071 | 2 | 78 | Hs.323308 | sprouty homolog 4 (Drosophila) /// similar to sprouty homolog 4 (Drosophila) | SPRY4 /// LOC653170 | 5q31.3 | |
1072 | 2 | 79 | Hs.323308 | sprouty homolog 4 (Drosophila) /// sprouty homolog 4 (Drosophila) | SPRY4 | 5q31.3 | ENSG00000187678 |
1073 | 2 | 80 | Hs.372938 | neurexin 2 | NRXN2 | 11q13 | ENSG00000110076 |
1074 | 2 | 81 | Hs.525781 | Sprouty-related, EVH1 domain containing 1 | SPRED1 | 15q14 | ENSG00000166068 |
1075 | 2 | 82 | Hs.368307 | neurexin 3 | NRXN3 | 14q31 | ENSG00000021645 |
1076 | 2 | 83 | Hs.518055 | leucine-rich repeats and immunoglobulin-like domains 1 | LRIG1 | 3p14 | ENSG00000144749 |
1077 | 2 | 84 | Hs.332708 | fibulin 5 | FBLN5 | 14q32.1 | ENSG00000140092 |
1078 | 2 | 85 | Hs.482730 | EGF-like repeats and discoidin I-like domains 3 | EDIL3 | 5q14 | ENSG00000164176 |
1079 | 2 | 86 | Hs.179704 | meprin A, alpha (PABA peptide hydrolase) | MEP1A | 6p12-p11 | ENSG00000112818 |
1080 | 2 | 87 | Hs.1274 | bone morphogenetic protein 1 | BMP1 | 8p21 | ENSG00000168487 |
1081 | 2 | 88 | Hs.106513 | tolloid-like 1 | TLL1 | 4q32-q33 | ENSG00000038295 |
1082 | 2 | 89 | Hs.154296 | tolloid-like 2 | TLL2 | 10q23-q24 | ENSG00000095587 |
1083 | 2 | 90 | Hs.465407 | neuropilin (NRP) and tolloid (TLL)-like 1 | NETO1 | 18q22-q23 | ENSG00000166342 |
1084 | 2 | 91 | Hs.444046 | neuropilin (NRP) and tolloid (TLL)-like 2 | NETO2 | 16q11 | ENSG00000171208 |
1085 | 2 | 92 | Hs.177959 | ADAM metallopeptidase domain 2 (fertilin beta) | ADAM2 | 8p11.2 | ENSG00000104755 |
1086 | 2 | 93 | Hs.98848 | ADAM metallopeptidase domain 3a (cyritestin 1) | ADAM3A | 8p21-p12 | |
1087 | 2 | 94 | Hs.97508 | ADAM metallopeptidase domain 6 | ADAM6 | 14q32.33 | |
1088 | 2 | 95 | Hs.116147 | ADAM metallopeptidase domain 7 | ADAM7 | 8p21.2 | ENSG00000069206 |
1089 | 2 | 96 | Hs.501574 | ADAM metallopeptidase domain 8 /// ADAM metallopeptidase domain 8 | ADAM8 | 10q26.3 | ENSG00000151651 |
Problems
Because of the need of sharing the synopsis the biggest problem is getting a synchronised Synopsis back if more than people download the list, edit it, and upload it back to the server.
All the different versions will lead to a unmanageable mess.
For that reason, it is indispensable to change the handling for the synopsis.
Collaborating on an excel sheet leads to a mess.
Requirements to new system
- moving genes or blocks of genes from one to an other pathway
- Adding/Deleting/Moving pathways
- Adding/Deleting/Moving subgroups of pathways
- Adding more complex annotations to genes/pathways/pathwaysubgroups
- Adding/Deleting/Moving genes. Whole blocks at once should be possible
- Versioning
- Every action has to logged with following information:
WHO has done WHAT at WHAT TIME - Every action must be restoreable. (Like the history mechanism in Wiki)
- Every action has to logged with following information:
- Keep a defined order, change an order
- For further analysis (like matching synopsis versus exeriments) excel is quite good.
--> support a synopsis download as excel.
In future, create online tools for matching. - user - rigths management --> use of Wiki - Account for login - required. (one account --> whole access)
- Visulatisation of Synopsis should be done as a navigation tree.
Check to example how it should look like: http://www.destroydrop.com/javascripts/tree/
Approaches
Approach | Advantage | Disadvantage |
Using Lipidnet form ISB | Many of the necessary functionalities are available;
Covers most problems like adding, deleting; Already has the desired structure. | No Code available; no single login;
No automatic upload for batch files. Slowly, some bugs; dependent on ISB. |
With Wiki | Easy to edit; everyone has the same account; a batch of genes is easy to add; | Difficult generating Excel files also importing Excel files -> writing parsers. Splitting of the whole list necessary; speed problems |
With adapted “Verfahrensliste” | A prototype can be rapidly made; easy export/import to/from Excel; | Some changes necessary for single login; every functionality has to be programmed by ourselves; |
With Excel files accessible via ftp-server | Initial working with the files is very easy; | Difficult to merge several version; no versions on dataset level only on file level |
With Excel files with CVS | Initial working with the files is very easy; | Difficult to merge several versions; no versions on dataset level only on file level; every client needs a special client tortoise-cvs; |
Googling for existing php-modules which implements a usable structure for displaying and working with the synopsis list | | |
Conclusion: We make a prototype with the “Verfahrensliste” and decide then.