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ropensci / biomartr

Genomic Data Retrieval with R
https://docs.ropensci.org/biomartr
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Example of csv file for biomatr #16

Closed NasDenis closed 7 years ago

NasDenis commented 7 years ago

Hi,

I am used to Vikodak and recently, the website is no longer active. Can I have an example for the raw data (.csv) to import into R for biomatr? I am interested in retrieving the functional annotation.

Thanks! =)

HajkD commented 7 years ago

Hi @NasDenis,

Many thanks for contacting me :)

Unfortunately, I am not familiar with Vikodak.

Could you please send me an example Vikodak workflow (.csv file as input?) for me to understand the format and usability? I am happy to see if I can help you to adjust your Vikodak workflow to the biomartr methodology.

Many thanks! Hajk

NasDenis commented 7 years ago

Hi,

Thank you for the prompt reply :) Vikodak was web-based and we uploaded data such as per attached and Vikodak will send email to us with the functional annotations (also as per attached). biomatr involved codings which I am not entirely good and confident on :(

I saw the steps listed in Github and is there by any chance there is a short codings to obtain the functional annotations?

Nas

On Thu, Aug 10, 2017 at 6:03 PM, Hajk-Georg Drost notifications@github.com wrote:

Hi @NasDenis https://github.com/nasdenis,

Many thanks for contacting me :)

Unfortunately, I am not familiar with Vikodak.

Could you please send me an example Vikodak workflow (.csv file as input?) for me to understand the format and usability? I am happy to see if I can help you to adjust your Vikodak workflow to the biomartr methodology.

Many thanks! Hajk

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/biomartr/issues/16#issuecomment-321508781, or mute the thread https://github.com/notifications/unsubscribe-auth/AddYcRfkJqmPlZ5GTCEvm-EKCI8KTZqPks5sWtWNgaJpZM4Oy_uW .

Pathway Search Result

Following object(s) was/were not found ec:1.2.99.2 ec:1.3.99.1 ko:#ff6699 ko:#ff9933 ko:#ffcfff ko:#ffefcc Sort by the pathway list Show all objects Station1_Dec14 ko01120 Microbial metabolism in diverse environments (102)

ko01100 Metabolic pathways (90)

ko01200 Carbon metabolism (87)

ko00720 Carbon fixation pathways in prokaryotes (70)

ko01130 Biosynthesis of antibiotics (65)

ko00640 Propanoate metabolism (43)

ko01110 Biosynthesis of secondary metabolites (36)

ko00620 Pyruvate metabolism (33)

ko00020 Citrate cycle (TCA cycle) (29)

ko00280 Valine, leucine and isoleucine degradation (24)

ko00650 Butanoate metabolism (24)

ko00630 Glyoxylate and dicarboxylate metabolism (23)

ko00680 Methane metabolism (22)

ko01212 Fatty acid metabolism (17)

ko00071 Fatty acid degradation (13)

ko00633 Nitrotoluene degradation (8)

ko00362 Benzoate degradation (8)

ko00380 Tryptophan metabolism (8)

ko00010 Glycolysis / Gluconeogenesis (8)

ko00310 Lysine degradation (8)

ko00061 Fatty acid biosynthesis (7)

ko00930 Caprolactam degradation (7)

ko01230 Biosynthesis of amino acids (7)

ko00670 One carbon pool by folate (6)

ko00660 C5-Branched dibasic acid metabolism (6)

ko01220 Degradation of aromatic compounds (6)

ko00410 beta-Alanine metabolism (6)

ko00523 Polyketide sugar unit biosynthesis (6)

ko00524 Neomycin, kanamycin and gentamicin biosynthesis (5)

ko04146 Peroxisome (5)

ko00710 Carbon fixation in photosynthetic organisms (5)

ko00281 Geraniol degradation (5)

ko00627 Aminobenzoate degradation (4)

ko01210 2-Oxocarboxylic acid metabolism (4)

ko04931 Insulin resistance (4)

ko00430 Taurine and hypotaurine metabolism (4)

ko00520 Amino sugar and nucleotide sugar metabolism (3)

ko01059 Biosynthesis of enediyne antibiotics (3)

ko02020 Two-component system (3)

ko00062 Fatty acid elongation (3)

ko00270 Cysteine and methionine metabolism (3)

ko03320 PPAR signaling pathway (3)

ko00830 Retinol metabolism (3)

ko00903 Limonene and pinene degradation (3)

ko01057 Biosynthesis of type II polyketide products (3)

ko01040 Biosynthesis of unsaturated fatty acids (3)

ko04152 AMPK signaling pathway (2)

ko00240 Pyrimidine metabolism (2)

ko00051 Fructose and mannose metabolism (2)

ko00254 Aflatoxin biosynthesis (2)

ko00592 alpha-Linolenic acid metabolism (2)

ko04922 Glucagon signaling pathway (2)

ko00626 Naphthalene degradation (2)

ko00623 Toluene degradation (2)

ko04910 Insulin signaling pathway (2)

ko00072 Synthesis and degradation of ketone bodies (1)

ko01056 Biosynthesis of type II polyketide backbone (1)

ko00290 Valine, leucine and isoleucine biosynthesis (1)

ko05211 Renal cell carcinoma (1)

ko04960 Aldosterone-regulated sodium reabsorption (1)

ko00260 Glycine, serine and threonine metabolism (1)

ko01523 Antifolate resistance (1)

ko00300 Lysine biosynthesis (1)

ko00966 Glucosinolate biosynthesis (1)

ko04964 Proximal tubule bicarbonate reclamation (1)

ko00900 Terpenoid backbone biosynthesis (1)

ko00480 Glutathione metabolism (1)

ko00253 Tetracycline biosynthesis (1)

ko04920 Adipocytokine signaling pathway (1)

ko00040 Pentose and glucuronate interconversions (1)

ko00404 Staurosporine biosynthesis (1)

ko00750 Vitamin B6 metabolism (1)

ko01502 Vancomycin resistance (1)

ko01051 Biosynthesis of ansamycins (1)

ko05200 Pathways in cancer (1)

ko00525 Acarbose and validamycin biosynthesis (1)

ko00360 Phenylalanine metabolism (1)

ko00120 Primary bile acid biosynthesis (1)

ko00140 Steroid hormone biosynthesis (1)

ko00642 Ethylbenzene degradation (1)

ko05010 Alzheimer's disease (1)

ko00400 Phenylalanine, tyrosine and tryptophan biosynthesis (1)

Station3 Pathway Search Result

Following object(s) was/were not found ec:1.2.99.2 ec:1.3.99.1 ko:#ff6699 ko:#ff9933 ko:#ffcfff ko:#ffefcc Sort by the pathway list Show all objects ko01120 Microbial metabolism in diverse environments (99)

ko01100 Metabolic pathways (87)

ko01200 Carbon metabolism (85)

ko00720 Carbon fixation pathways in prokaryotes (67)

ko01130 Biosynthesis of antibiotics (62)

ko00640 Propanoate metabolism (43)

ko01110 Biosynthesis of secondary metabolites (33)

ko00620 Pyruvate metabolism (33)

ko00020 Citrate cycle (TCA cycle) (26)

ko00650 Butanoate metabolism (24)

ko00280 Valine, leucine and isoleucine degradation (24)

ko00630 Glyoxylate and dicarboxylate metabolism (23)

ko00680 Methane metabolism (22)

ko01212 Fatty acid metabolism (17)

ko00071 Fatty acid degradation (13)

ko00633 Nitrotoluene degradation (8)

ko00010 Glycolysis / Gluconeogenesis (8)

ko00380 Tryptophan metabolism (8)

ko00310 Lysine degradation (8)

ko00362 Benzoate degradation (8)

ko01230 Biosynthesis of amino acids (7)

ko00061 Fatty acid biosynthesis (7)

ko00930 Caprolactam degradation (7)

ko00410 beta-Alanine metabolism (6)

ko01220 Degradation of aromatic compounds (6)

ko00670 One carbon pool by folate (6)

ko00523 Polyketide sugar unit biosynthesis (6)

ko00660 C5-Branched dibasic acid metabolism (6)

ko04146 Peroxisome (5)

ko00524 Neomycin, kanamycin and gentamicin biosynthesis (5)

ko00281 Geraniol degradation (5)

ko00710 Carbon fixation in photosynthetic organisms (5)

ko00430 Taurine and hypotaurine metabolism (4)

ko04931 Insulin resistance (4)

ko00627 Aminobenzoate degradation (4)

ko01210 2-Oxocarboxylic acid metabolism (4)

ko01040 Biosynthesis of unsaturated fatty acids (3)

ko02020 Two-component system (3)

ko03320 PPAR signaling pathway (3)

ko01057 Biosynthesis of type II polyketide products (3)

ko00270 Cysteine and methionine metabolism (3)

ko01059 Biosynthesis of enediyne antibiotics (3)

ko00520 Amino sugar and nucleotide sugar metabolism (3)

ko00062 Fatty acid elongation (3)

ko00903 Limonene and pinene degradation (3)

ko00830 Retinol metabolism (3)

ko04910 Insulin signaling pathway (2)

ko00592 alpha-Linolenic acid metabolism (2)

ko04152 AMPK signaling pathway (2)

ko00254 Aflatoxin biosynthesis (2)

ko00051 Fructose and mannose metabolism (2)

ko00240 Pyrimidine metabolism (2)

ko00626 Naphthalene degradation (2)

ko04922 Glucagon signaling pathway (2)

ko00623 Toluene degradation (2)

ko00900 Terpenoid backbone biosynthesis (1)

ko00140 Steroid hormone biosynthesis (1)

ko00525 Acarbose and validamycin biosynthesis (1)

ko00253 Tetracycline biosynthesis (1)

ko04964 Proximal tubule bicarbonate reclamation (1)

ko01502 Vancomycin resistance (1)

ko05211 Renal cell carcinoma (1)

ko01051 Biosynthesis of ansamycins (1)

ko00290 Valine, leucine and isoleucine biosynthesis (1)

ko01523 Antifolate resistance (1)

ko00260 Glycine, serine and threonine metabolism (1)

ko00404 Staurosporine biosynthesis (1)

ko00966 Glucosinolate biosynthesis (1)

ko00750 Vitamin B6 metabolism (1)

ko05200 Pathways in cancer (1)

ko00120 Primary bile acid biosynthesis (1)

ko04960 Aldosterone-regulated sodium reabsorption (1)

ko00072 Synthesis and degradation of ketone bodies (1)

ko00642 Ethylbenzene degradation (1)

ko05010 Alzheimer's disease (1)

ko00400 Phenylalanine, tyrosine and tryptophan biosynthesis (1)

ko00480 Glutathione metabolism (1)

ko00040 Pentose and glucuronate interconversions (1)

ko01056 Biosynthesis of type II polyketide backbone (1)

ko00300 Lysine biosynthesis (1)

ko00360 Phenylalanine metabolism (1)

ko04920 Adipocytokine signaling pathway (1)

Station3 Pathway Search Result

Following object(s) was/were not found ec:1.2.99.2 ec:1.3.99.1 ko:#cc3366 ko:#ff6699 ko:#ff9933 ko:#ffcfff ko:#ffefcc Sort by the pathway list Show all objects ko01120 Microbial metabolism in diverse environments (101)

ko01100 Metabolic pathways (88)

ko01200 Carbon metabolism (88)

ko00720 Carbon fixation pathways in prokaryotes (69)

ko01130 Biosynthesis of antibiotics (62)

ko00640 Propanoate metabolism (43)

ko00620 Pyruvate metabolism (33)

ko01110 Biosynthesis of secondary metabolites (33)

ko00020 Citrate cycle (TCA cycle) (26)

ko00650 Butanoate metabolism (25)

ko00280 Valine, leucine and isoleucine degradation (24)

ko00630 Glyoxylate and dicarboxylate metabolism (23)

ko00680 Methane metabolism (22)

ko01212 Fatty acid metabolism (17)

ko00071 Fatty acid degradation (13)

ko00010 Glycolysis / Gluconeogenesis (8)

ko00380 Tryptophan metabolism (8)

ko00310 Lysine degradation (8)

ko00633 Nitrotoluene degradation (8)

ko00362 Benzoate degradation (8)

ko00930 Caprolactam degradation (7)

ko00061 Fatty acid biosynthesis (7)

ko01230 Biosynthesis of amino acids (7)

ko00523 Polyketide sugar unit biosynthesis (6)

ko01220 Degradation of aromatic compounds (6)

ko00670 One carbon pool by folate (6)

ko00410 beta-Alanine metabolism (6)

ko00660 C5-Branched dibasic acid metabolism (6)

ko04146 Peroxisome (5)

ko00710 Carbon fixation in photosynthetic organisms (5)

ko00524 Neomycin, kanamycin and gentamicin biosynthesis (5)

ko00281 Geraniol degradation (5)

ko01210 2-Oxocarboxylic acid metabolism (4)

ko00430 Taurine and hypotaurine metabolism (4)

ko04931 Insulin resistance (4)

ko00627 Aminobenzoate degradation (4)

ko00270 Cysteine and methionine metabolism (3)

ko00903 Limonene and pinene degradation (3)

ko02020 Two-component system (3)

ko01057 Biosynthesis of type II polyketide products (3)

ko03320 PPAR signaling pathway (3)

ko00062 Fatty acid elongation (3)

ko01040 Biosynthesis of unsaturated fatty acids (3)

ko00830 Retinol metabolism (3)

ko00520 Amino sugar and nucleotide sugar metabolism (3)

ko01059 Biosynthesis of enediyne antibiotics (3)

ko00051 Fructose and mannose metabolism (2)

ko00254 Aflatoxin biosynthesis (2)

ko00623 Toluene degradation (2)

ko00592 alpha-Linolenic acid metabolism (2)

ko04910 Insulin signaling pathway (2)

ko00240 Pyrimidine metabolism (2)

ko00626 Naphthalene degradation (2)

ko04152 AMPK signaling pathway (2)

ko04922 Glucagon signaling pathway (2)

ko04920 Adipocytokine signaling pathway (1)

ko01056 Biosynthesis of type II polyketide backbone (1)

ko05211 Renal cell carcinoma (1)

ko00750 Vitamin B6 metabolism (1)

ko04960 Aldosterone-regulated sodium reabsorption (1)

ko00480 Glutathione metabolism (1)

ko00642 Ethylbenzene degradation (1)

ko00290 Valine, leucine and isoleucine biosynthesis (1)

ko05200 Pathways in cancer (1)

ko01502 Vancomycin resistance (1)

ko00140 Steroid hormone biosynthesis (1)

ko05010 Alzheimer's disease (1)

ko00404 Staurosporine biosynthesis (1)

ko04964 Proximal tubule bicarbonate reclamation (1)

ko01523 Antifolate resistance (1)

ko00120 Primary bile acid biosynthesis (1)

ko00360 Phenylalanine metabolism (1)

ko00253 Tetracycline biosynthesis (1)

ko00900 Terpenoid backbone biosynthesis (1)

ko00400 Phenylalanine, tyrosine and tryptophan biosynthesis (1)

ko00260 Glycine, serine and threonine metabolism (1)

ko00300 Lysine biosynthesis (1)

ko00966 Glucosinolate biosynthesis (1)

ko00072 Synthesis and degradation of ketone bodies (1)

ko00525 Acarbose and validamycin biosynthesis (1)

ko01051 Biosynthesis of ansamycins (1)

ko00040 Pentose and glucuronate interconversions (1)

HajkD commented 7 years ago

Hi @NasDenis,

Ah ok, I see :)

Have you tried the web tools Kegg or Ensembl BioMart ? They provide a user interface for retrieving functional annotation information.

The biomartr package is designed for the automation of the functional annotation retrieval process. So unfortunately, there is no "easier" way to retrieve functional annotations with biomartr than is described in the tutorial vignettes. I am sorry :(

Hopefully, the KeGG or Ensembl BioMart web user interfaces are helpful for you?

Please keep me posted.

Many thanks and best wishes, Hajk

NasDenis commented 7 years ago

Hi,

Thank you so much! I will try with Kegg and Ensembl BioMart and keep you updated :)

Nas

On Fri, Aug 11, 2017 at 5:52 PM, Hajk-Georg Drost notifications@github.com wrote:

Hi @NasDenis https://github.com/nasdenis,

Ah ok, I see :)

Have you tried the web tools Kegg http://www.genome.jp/kegg/pathway.html or Ensembl BioMart http://www.ensembl.org/info/website/tutorials/index.html ? They provide a user interface for retrieving functional annotation information.

The biomartr package is designed for the automation of the functional annotation retrieval process. So unfortunately, there is no "easier" way to retrieve functional annotations with biomartr than is described in the tutorial vignettes. I am sorry :(

Hopefully, the KeGG or Ensembl BioMart web user interfaces are helpful for you?

Please keep me posted.

Many thanks and best wishes, Hajk

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/biomartr/issues/16#issuecomment-321772303, or mute the thread https://github.com/notifications/unsubscribe-auth/AddYcZRU5Q3gvocYXs7C4Xfc6AHElNTWks5sXCRsgaJpZM4Oy_uW .

NasDenis commented 7 years ago

Hi,

Kegg is a database providing IDs to pathways etc and not applicable to trying to find the function in my samples. I have tried the rest (I tried all in OMIC tools but to no avail). The service is either looking for the function in their database based on the IDs that we want from KEGG. Do you know any other services?

Here's the list I have tried :- Cofeco MBrole Panther Woods Trapid Real Time Genomics CATH Scripps Target express GoMapMan

Nas

On Sat, Aug 12, 2017 at 8:20 AM, Nas Denis nasdenis82@gmail.com wrote:

Hi,

Thank you so much! I will try with Kegg and Ensembl BioMart and keep you updated :)

Nas

On Fri, Aug 11, 2017 at 5:52 PM, Hajk-Georg Drost < notifications@github.com> wrote:

Hi @NasDenis https://github.com/nasdenis,

Ah ok, I see :)

Have you tried the web tools Kegg http://www.genome.jp/kegg/pathway.html or Ensembl BioMart http://www.ensembl.org/info/website/tutorials/index.html ? They provide a user interface for retrieving functional annotation information.

The biomartr package is designed for the automation of the functional annotation retrieval process. So unfortunately, there is no "easier" way to retrieve functional annotations with biomartr than is described in the tutorial vignettes. I am sorry :(

Hopefully, the KeGG or Ensembl BioMart web user interfaces are helpful for you?

Please keep me posted.

Many thanks and best wishes, Hajk

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/biomartr/issues/16#issuecomment-321772303, or mute the thread https://github.com/notifications/unsubscribe-auth/AddYcZRU5Q3gvocYXs7C4Xfc6AHElNTWks5sXCRsgaJpZM4Oy_uW .

HajkD commented 7 years ago

Hi Nas,

Unfortunately not :(

I hope you can find a tool that suits you!

Best wishes Hajk

NasDenis commented 7 years ago

Hi,

Still none. So I will try biomatr (cross fingers ;)). Can I start by using cmd?

Nas

On Aug 31, 2017, at 7:34 PM, Hajk-Georg Drost notifications@github.com wrote:

Hi Nas,

Unfortunately not :(

I hope you can find a tool that suits you!

Best wishes Hajk

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/biomartr/issues/16#issuecomment-326268856, or mute the thread https://github.com/notifications/unsubscribe-auth/AddYcUEGMBK7-MKpJQ9vEfODFNQ2lQ6Rks5sdpo0gaJpZM4Oy_uW.