From 985682da205e4ff76d3d4fc02572c395daa07d37 Mon Sep 17 00:00:00 2001 From: Chris Hunter Date: Tue, 13 Feb 2024 20:38:57 +0000 Subject: [PATCH] Update extensions.md - replaced name based extension URLs to ID based URLs to link out to automated documentation pages - added hyperlinks to associated paper DOIs --- pages/standards/extensions.md | 48 +++++++++++++++++------------------ 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/pages/standards/extensions.md b/pages/standards/extensions.md index dbd7359..3d67fc4 100644 --- a/pages/standards/extensions.md +++ b/pages/standards/extensions.md @@ -12,52 +12,52 @@ For the complete documentation on each checklist, extension and individual term ## Current Extensions (packages) These are the current set of environmental packages: - * [MIxS-agriculture](https://genomicsstandardsconsortium.github.io/mixs/Agriculture/) (J. P. Dundore-Arias, et.al 2020) + * [MIxS-agriculture](https://genomicsstandardsconsortium.github.io/mixs/0016018/) (J. P. Dundore-Arias, et.al 2020 [link to paper](https://doi.org/10.1094/PBIOMES-09-19-0051-P) ) - * [MIxS-air](https://genomicsstandardsconsortium.github.io/mixs/air) (Yilmaz et al. 2011) + * [MIxS-air](https://genomicsstandardsconsortium.github.io/mixs/0016000) (Yilmaz et al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-built environment](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironment) (Glass et al. 2014) + * [MIxS-built environment](https://genomicsstandardsconsortium.github.io/mixs/0016001) (Glass et al. 2014 [link to paper](https://doi.org/10.1038/ismej.2013.176) ) - * [MIxS-food-animal and animal feed](https://genomicsstandardsconsortium.github.io/mixs/FoodAnimalAndAnimalFeed) + * [MIxS-food-animal and animal feed](https://genomicsstandardsconsortium.github.io/mixs/0016019) - * [MIxS-food-farm environment](https://genomicsstandardsconsortium.github.io/mixs/FoodFarmEnvironment/) + * [MIxS-food-farm environment](https://genomicsstandardsconsortium.github.io/mixs/0016020/) - * [MIxS-food-food production facility](https://genomicsstandardsconsortium.github.io/mixs/FoodFoodProductionFacility) + * [MIxS-food-food production facility](https://genomicsstandardsconsortium.github.io/mixs/0016021) - * [MIxS-food-human foods](https://genomicsstandardsconsortium.github.io/mixs/FoodHumanFoods) + * [MIxS-food-human foods](https://genomicsstandardsconsortium.github.io/mixs/0016022) - * [MIxS-host-associated](https://genomicsstandardsconsortium.github.io/mixs/HostAssociated) (Yilmaz et al. 2011) + * [MIxS-host-associated](https://genomicsstandardsconsortium.github.io/mixs/0016002) (Yilmaz et al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-human-associated](https://genomicsstandardsconsortium.github.io/mixs/HumanAssociated) (Yilmaz et al. 2011) + * [MIxS-human-associated](https://genomicsstandardsconsortium.github.io/mixs/0016003) (Yilmaz et al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-human-gut](https://genomicsstandardsconsortium.github.io/mixs/HumanGut) (Yilmaz et al. 2011) + * [MIxS-human-gut](https://genomicsstandardsconsortium.github.io/mixs/0016004) (Yilmaz et al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-human-oral](https://genomicsstandardsconsortium.github.io/mixs/HumanOral) (Yilmaz et al. 2011) + * [MIxS-human-oral](https://genomicsstandardsconsortium.github.io/mixs/0016005) (Yilmaz et al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-human-skin](https://genomicsstandardsconsortium.github.io/mixs/HumanSkin) (Yilmaz et al. 2011) + * [MIxS-human-skin](https://genomicsstandardsconsortium.github.io/mixs/0016006) (Yilmaz et al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-human-vaginal](https://genomicsstandardsconsortium.github.io/mixs/HumanVaginal) (Yilmaz et al. 2011) + * [MIxS-human-vaginal](https://genomicsstandardsconsortium.github.io/mixs/0016007) (Yilmaz et al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-hydrocarbon resources-cores](https://genomicsstandardsconsortium.github.io/mixs/HydrocarbonResourcesCores) (Tsesmetzis et al. 2016) + * [MIxS-hydrocarbon resources-cores](https://genomicsstandardsconsortium.github.io/mixs/0016015) (Tsesmetzis et al. 2016 [link to paper](https://doi.org/10.1186/s40793-016-0203-5) ) - * [MIxS-hydrocarbon resources-fluids/swabs](https://genomicsstandardsconsortium.github.io/mixs/HydrocarbonResourcesFluidsSwabs) (Tsesmetzis et al. 2016) . + * [MIxS-hydrocarbon resources-fluids/swabs](https://genomicsstandardsconsortium.github.io/mixs/0016016) (Tsesmetzis et al. 2016 [link to paper](https://doi.org/10.1186/s40793-016-0203-5) ) - * [MIxS-microbial mat/biofilm](https://genomicsstandardsconsortium.github.io/mixs/MicrobialMatBiofilm) (Yilmaz et al. 2011) + * [MIxS-microbial mat/biofilm](https://genomicsstandardsconsortium.github.io/mixs/0016008) (Yilmaz et al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-miscellaneous natural or artificial environment](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironment) (Yilmaz et al. 2011) + * [MIxS-miscellaneous natural or artificial environment](https://genomicsstandardsconsortium.github.io/mixs/0016009) (Yilmaz et al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-plant-associated](https://genomicsstandardsconsortium.github.io/mixs/PlantAssociated) (Yilmaz et.al. 2011) + * [MIxS-plant-associated](https://genomicsstandardsconsortium.github.io/mixs/0016010) (Yilmaz et.al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-sediment](https://genomicsstandardsconsortium.github.io/mixs/Sediment) (Yilmaz et.al. 2011) + * [MIxS-sediment](https://genomicsstandardsconsortium.github.io/mixs/0016011) (Yilmaz et.al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-soil](https://genomicsstandardsconsortium.github.io/mixs/Soil) (Yilmaz et.al. 2011) + * [MIxS-soil](https://genomicsstandardsconsortium.github.io/mixs/0016012) (Yilmaz et.al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-symbiont-associated](https://genomicsstandardsconsortium.github.io/mixs/SymbiontAssociated) (Jorge et al., 2022) + * [MIxS-symbiont-associated](https://genomicsstandardsconsortium.github.io/mixs/0016023) (Jorge et al., 2022 [link to paper](https://doi.org/10.1038/s43705-022-00092-w) ) - * [MIxS-wastewater/sludge](https://genomicsstandardsconsortium.github.io/mixs/WastewaterSludge) (Yilmaz et.al. 2011) + * [MIxS-wastewater/sludge](https://genomicsstandardsconsortium.github.io/mixs/0016013) (Yilmaz et.al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) - * [MIxS-water](https://genomicsstandardsconsortium.github.io/mixs/Water) (Yilmaz et.al. 2011) + * [MIxS-water](https://genomicsstandardsconsortium.github.io/mixs/0016014) (Yilmaz et.al. 2011 [link to paper](https://doi.org/10.1038/nbt.1823) ) [Dundore-Arias, JP. et al., "Community-Driven Metadata Standards for Agricultural Microbiome Research" Phytobiomes Journal 2020 4:2, 115-121 DOI:10.1094/PBIOMES-09-19-0051-P](https://doi.org/10.1094/PBIOMES-09-19-0051-P). @@ -68,7 +68,7 @@ These are the current set of environmental packages: [Tsesmetzis N. et al., "MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources" Stand Genomic Sci. 2016 Oct 12;11:78. doi: 10.1186/s40793-016-0203-5. eCollection 2016.](https://doi.org/10.1186/s40793-016-0203-5) -[Yilmaz, P. et al., "Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications." Nature biotechnology vol. 29,5 (2011): 415-20. doi:10.1038/nbt.1823](https://doi.org/10.1038/nbt.1823). +[Yilmaz, P. et al., "Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications." Nature biotechnology vol. 29,5 (2011): 415-20. doi:10.1038/nbt.1823](https://doi.org/10.1038/nbt.1823)